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b/_modules/ensembl/tools/anno/protein_annotation/genblast.html @@ -0,0 +1,615 @@ + + + + + + + ensembl.tools.anno.protein_annotation.genblast — ensembl-anno 0.1 documentation + + + + + + + + + + + +
+
+
+ +
+
+
+ +

Source code for ensembl.tools.anno.protein_annotation.genblast

+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""
+GenBlast identifies homologous gene sequences in genomic databases.
+One of the key features of GenBlast is its flexibility to handle
+comparative genomics tasks and accurately identify homologs even when
+the sequences have undergone significant evolutionary changes.
+This capability makes it a valuable resource for researchers studying gene
+evolution, gene families, and gene function across diverse species.
+GenBlast has been widely used in various genomic analyses and is available as
+a standalone command-line tool or as part of different bioinformatics pipelines.
+Researchers in the field of comparative genomics and gene function analysis
+often rely on GenBlast to perform sensitive homology searches and obtain
+valuable insights into the evolutionary relationships and functional conservation
+of genes in different organisms.
+
+
+She, R., Chu, J.S., Uyar, B., Wang, J., Wang, K., and Chen, N. (2011).
+GenBlastA: enabling BLAST to identify homologous gene sequences.
+Genome Res., 21(5): 936-949.
+"""
+__all__ = ["run_genblast"]
+
+import logging
+import logging.config
+import multiprocessing
+import os
+from pathlib import Path
+import random
+import re
+import shutil
+import signal
+import subprocess
+from typing import List
+import argschema
+
+from ensembl.tools.anno.utils._utils import (
+    check_exe,
+    create_dir,
+    check_gtf_content,
+)
+
+logger = logging.getLogger(__name__)
+
+
+
[docs]def run_genblast(#pylint:disable=dangerous-default-value
+    masked_genome: Path,
+    output_dir: Path,
+    protein_dataset: Path,
+    max_intron_length: int,
+    genblast_timeout_secs: int = 10800,
+    genblast_bin: Path = Path("genblast"),
+    convert2blastmask_bin: Path = Path("convert2blastmask"),
+    makeblastdb_bin: Path = Path("makeblastdb"),
+    num_threads: int = 1,
+    protein_set: str = ["uniprot", "orthodb"],
+) -> None:
+    """
+    
+    Executes GenBlast on genomic slices
+    
+            :param masked_genome: Masked genome file path.
+            :type masked_genome: Path
+            :param output_dir: Working directory path.
+            :type output_dir: Path
+            :param protein_dataset: Protein dataset (Uniprot/OrthoDb) path.
+            :type protein_dataset: Path
+            :param genblast_timeout_secs: Time for timeout (sec).
+            :type genblast_timeout_secs: int, default 10800
+            :param max_intron_length: Maximum intron length.
+            :type max_intron_length: int 
+            :param genblast_bin: Software path.
+            :type genblast_bin: Path, default genblast
+            :param convert2blastmask_bin: Software path.
+            :type convert2blastmask_bin: Path, default convert2blastmask
+            :param makeblastdb_bin: Software path.
+            :type makeblastdb_bin: Path, default makeblastdb
+            :param genblast_timeout: seconds
+            :type genblast_timeout: int, default 1
+            :param num_threads: int, number of threads.
+            :type num_threads: int, default 1 
+            :param protein_set: Source 
+            :type str: ["uniprot", "orthodb"]
+            
+            :return: None
+            :rtype: None
+            
+    """
+
+    check_exe(genblast_bin)
+    check_exe(convert2blastmask_bin)
+    check_exe(makeblastdb_bin)
+    if protein_set == "uniprot":
+        genblast_dir = create_dir(output_dir, "uniprot_output")
+    elif protein_set == "orthodb":
+        genblast_dir = create_dir(output_dir, "orthodb_output")
+    output_file = genblast_dir / "annotation.gtf"
+    if output_file.exists():
+        transcript_count = check_gtf_content(output_file, "transcript")
+        if transcript_count > 0:
+            logger.info("Genblast gtf file exists, skipping analysis")
+            return
+    logging.info(Path(f"{output_dir}/alignscore.txt"))
+    if not Path(f"{genblast_dir}/alignscore.txt").exists():
+        # Get the repo directory
+        repo_root_dir = Path(__file__).parents[6]
+        shutil.copy(Path(f"{repo_root_dir}/data/alignscore.txt"), genblast_dir)
+
+    if not masked_genome.exists():
+        raise IOError(f"Masked genome file does not exist: {masked_genome}")
+    if not protein_dataset.exists():
+        raise IOError(f"Protein file does not exist: {protein_dataset}")
+    asnb_file = Path(f"{masked_genome}.asnb")
+    if asnb_file.exists():
+        logger.info("Found an existing asnb, so will skip convert2blastmask")
+    else:
+        _run_convert2blastmask(convert2blastmask_bin, masked_genome, asnb_file)
+    _run_makeblastdb(makeblastdb_bin, masked_genome, asnb_file)
+    batched_protein_files = _split_protein_file(
+        protein_dataset, genblast_dir, num_threads
+    )
+    pool = multiprocessing.Pool(num_threads)  # pylint:disable=consider-using-with
+    for batched_protein_file in batched_protein_files:
+        pool.apply_async(
+            _multiprocess_genblast,
+            args=(
+                batched_protein_file,
+                masked_genome,
+                genblast_bin,
+                genblast_timeout_secs,
+                max_intron_length,
+            ),
+        )
+    pool.close()
+    pool.join()
+    _generate_genblast_gtf(genblast_dir)
+    for i in range(0, 10):
+        shutil.rmtree(genblast_dir / f"bin_{i}")
+    logger.info("Completed running GenBlast")

+
+
+def _multiprocess_genblast(
+    protein_file: Path,
+    masked_genome: Path,
+    genblast_bin: Path,
+    genblast_timeout: int,
+    max_intron_length: int,
+):
+    """
+    Executes GenBlast on genomic slice
+    Args:
+            protein_file: Path of a single batched file.
+            masked_genome : Masked genome file path.
+            genblast_bin : Software path.
+            genblast_timeout_secs: Time for timeout (sec).
+            max_intron_length: Maximum intron length.
+            Command line options:
+            -P	Search program used to produce HSPs,
+                can be either "blast" or "wublast", default is "blast",
+                optional
+            -p	specifies the program option of genBlast: genblasta or genblastg
+            -q	List of query sequences to blast, must be in fasta format,
+                required
+            -t	The target database of genomic sequences in fasta format,
+                required
+            -g	parameter for blast: Perform gapped alignment (T/F)
+                [default: F], optional
+            -d	parameter for genBlast: maximum allowed distance between HSPs
+                within the same gene, a non-negative integer [default: 100000],
+                optional
+            -r	parameter for genBlast: number of ranks in the output,
+                a positive integer, optional
+            -e	parameter for blast: The e-value, [default: 1e-2],
+                optional
+            -c	parameter for genBlast: minimum percentage of query gene
+                coverage in the output, between 0 and 1 (e.g. for 50%
+                gene coverage, use "0.5"), optional
+            -W	parameter for blast: Set word size, 0 means using blast default [default: 0],
+                optional
+            -scodon The number of base pairs to search for start codon within the region of HSP
+                        group (inside the first HSP). If not specified, default is 15.
+            -i	parameter for genBlastG: minimum intron length, optional.
+                If not specified, the default value is 15.
+            -x	parameter for genBlastG: minimum internal exon length, optional.
+                If not specified, default is 20.
+            -n	parameter for genBlastG: maximum number of splice sites per region, optional.
+                If not specified, default is 20.
+            -gff	output options: turn on GFF output
+            -o	output filename, optional. If not specified, the output
+                will be the same as the query filename with ".gblast"
+                extension.
+            -pid turn on final alignment PID computation (global alignment between predicted
+                gene and query) in output.
+            -softmask	With this option NCBI blast will create a masking library,
+                you need to use it when blasting against a whole genome
+    """
+    logger.info("Running GenBlast on : %s", protein_file)
+
+    genblast_cmd = [
+        str(genblast_bin),
+        "-p",
+        "genblastg",
+        "-q",
+        str(protein_file),
+        "-t",
+        str(masked_genome),
+        "-g",
+        "T",
+        "-pid",
+        "-r",
+        "1",
+        "-P",
+        "blast",
+        "-gff",
+        "-e",
+        "1e-1",
+        "-c",
+        "0.8",
+        "-W",
+        "3",
+        "-softmask",
+        "-scodon",
+        "50",
+        "-i",
+        "30",
+        "-x",
+        "10",
+        "-n",
+        "30",
+        "-d",
+        str(max_intron_length),
+        "-o",
+        str(protein_file),
+    ]
+
+    logger.info(" ".join(genblast_cmd))
+    # Using the child process termination as described here:
+    # https://alexandra-zaharia.github.io/posts/kill-subprocess
+    # -and-its-children-on-timeout-python/
+    try:
+        p = subprocess.Popen(# pylint:disable=consider-using-with
+            genblast_cmd, start_new_session=True
+        )
+        p.wait(timeout=genblast_timeout)
+    except subprocess.TimeoutExpired:
+        logger.error("Timeout reached for file: %s \n", protein_file)
+        subprocess.run(# pylint:disable=subprocess-run-check
+            ["touch", (Path(f"{protein_file}.except"))]
+        )
+        os.killpg(os.getpgid(p.pid), signal.SIGTERM)
+
+
+def _generate_genblast_gtf(genblast_dir: Path) -> None:
+    """
+    Collect output from geneblast and create the final gtf file
+    genblast_dir: Working directory path.
+    """
+    logging.info("AAAAA  _generate_genblast_gtf")
+    output_file = genblast_dir / "annotation.gtf"
+    with open(output_file, "w+", encoding="utf8") as file_out:
+        genblast_extension = "_1.1c_2.3_s1_0_16_1"
+        for path in genblast_dir.rglob("*"):
+            # for root, dirs, files in os.walk(genblast_dir):
+            # for genblast_file in files:
+            # genblast_file = os.path.join(root, genblast_file)
+            if path.is_file() and path.suffix == ".gff":
+                gtf_string = _convert_genblast_gff_to_gtf(path)
+                file_out.write(gtf_string)
+            elif path.is_file() and path.suffix in (
+                ".fa.blast",
+                ".fa.blast.report",
+                genblast_extension,
+            ):
+                path.unlink()
+
+
+def _split_protein_file(
+    protein_dataset: Path, output_dir: Path, batch_size: int = 20
+) -> List:
+    """
+    The protein dataset file is splitted by a number of sequence equals to the batch_size
+    in batch files stored in 10 output directories.
+    protein_dataset : Path for the protein dataset.
+    output_dir : Output directory path.
+    batch_size : Size of the batch, it needs to be equals to the number of threads
+    to parallelise the sequence processing for each file.
+    """
+    batched_protein_files = []
+
+    for i in range(0, 10):
+        create_dir(output_dir, (f"bin_{i}"))
+    with open(protein_dataset,"r", encoding="utf8") as file_in:
+        seq_count = 0
+        batch_count = 0
+        current_record = ""
+        initial_seq = True
+        for line in file_in:
+            match = re.search(r">(.+)$", line)
+            # match header and is not first sequence, if the number of stored sequences in each file equals
+            # the number of batch_size, a new file will be created and the current_record reset
+            if match and not initial_seq and seq_count % batch_size == 0:
+                bin_num = random.randint(0, 9)
+                batch_file = output_dir / f"bin_{bin_num}" / f"{batch_count}.fa"
+                with batch_file.open("w+") as file_out:
+                    file_out.write(current_record)
+                batch_count += 1
+                seq_count += 1
+                current_record = line
+                batched_protein_files.append(batch_file)
+            # match header and is the first sequence
+            elif match:
+                current_record += line
+                initial_seq = False
+                seq_count += 1
+            # other lines
+            else:
+                current_record += line
+
+        if current_record:
+            bin_num = random.randint(0, 9)
+            batch_file = output_dir / f"bin_{bin_num}" / f"{batch_count}.fa"
+            with batch_file.open("w+") as file_out:
+                file_out.write(current_record)
+            batched_protein_files.append(batch_file)
+    return batched_protein_files
+
+
+def _run_convert2blastmask(
+    convert2blastmask_bin: Path, masked_genome: Path, asnb_file: Path
+) -> None:
+    """
+    Convert masking information in lower-case masked FASTA input to file
+    formats suitable for makeblastdb.
+    convert2blastmask_bin : Software path.
+    masked_genome: Path of masked genome file.
+    asnb_file: Path of assembly file.
+    """
+    logger.info("Running convert2blastmask prior to GenBlast:")
+    cmd = [
+        str(convert2blastmask_bin),
+        "-in",
+        str(masked_genome),
+        "-parse_seqids",
+        "-masking_algorithm",  # mask_program_name
+        "other",
+        "-masking_options",  # mask_program_options
+        '"REpeatDetector, default"',
+        "-outfmt",  # output_format
+        "maskinfo_asn1_bin",
+        "-out",
+        str(asnb_file),
+    ]
+    logger.info(" ".join(cmd))
+    subprocess.run(cmd, check=True)
+    logger.info("Completed running convert2blastmask")
+
+
+def _run_makeblastdb(makeblastdb_bin: Path, masked_genome: Path, asnb_file: Path) -> None:
+    """
+    Application to create BLAST databases.
+    makeblastdb_bin : Software path.
+    masked_genome: Path of masked genome file.
+    asnb_file: Path of assembly file.
+    """
+    logger.info("Running makeblastdb prior to GenBlast")
+    subprocess.run(  # pylint:disable=subprocess-run-check
+        [
+            str(makeblastdb_bin),
+            "-in",
+            str(masked_genome),
+            "-dbtype",  # molecule_type
+            "nucl",
+            "-parse_seqids",
+            "-mask_data",
+            str(asnb_file),
+            "-max_file_sz",  # number_of_bytes
+            "10000000000",
+        ]
+    )
+    logger.info("Completed running makeblastdb")
+
+
+def _convert_genblast_gff_to_gtf(gff_file: Path) -> str:
+    """
+    Convert the content of gtf file in gff format
+    gff_file: Path for the gff file
+    """
+    gtf_string = ""
+    with open(gff_file, "r", encoding="utf8") as file_in:
+        for line in file_in:
+            results = line.split()
+            if len(results) == 9:
+                results[2] = "exon" if results[2] == "coding_exon" else results[2]
+                attributes = _set_genblast_attributes(str(results[8]), str(results[2]))
+                results[8] = attributes
+                converted_line = "\t".join(results)
+                gtf_string += converted_line + "\n"
+    return gtf_string
+
+
+def _set_genblast_attributes(attributes: str, feature_type: str) -> str:
+    """
+    Given the list of attributes in the genblast output,
+    define the new attributes for the gtf file.
+    attributes: GenBlast attribute list
+    feature_type: transcript or exon
+    Example genBlast output #pylint: disable=line-too-long, trailing-whitespace
+    1       genBlastG       transcript      131128674       131137049       252.729 -       .       ID=259447-R1-1-A1;Name=259447;PID=84.65;Coverage=94.22;Note=PID:84.65-Cover:94.22
+    1       genBlastG       coding_exon     131137031       131137049       .       -       .       ID=259447-R1-1-A1-E1;Parent=259447-R1-1-A1
+    1       genBlastG       coding_exon     131136260       131136333       .       -       .       ID=259447-R1-1-A1-E2;Parent=259447-R1-1-A1
+    1       genBlastG       coding_exon     131128674       131130245       .       -       .       ID=259447-R1-1-A1-E3;Parent=259447-R1-1-A1
+    """
+    converted_attributes = ""
+    split_attributes = attributes.split(";")
+    if feature_type == "transcript":
+        match = re.search(r"Name\=(.+)$", split_attributes[1])
+        assert match
+        name = match.group(1)
+        converted_attributes = f'gene_id "{name}"; transcript_id "{name}";'
+    elif feature_type == "exon":
+        match = re.search(r"\-E(\d+);Parent\=(.+)\-R\d+\-\d+\-", attributes)
+        assert match
+        exon_rank = match.group(1)
+        name = match.group(2)
+        converted_attributes = (
+            f'gene_id "{name}"; transcript_id "{name}"; exon_number "{exon_rank}";'
+        )
+
+    return converted_attributes
+
+
+class InputSchema(argschema.ArgSchema):
+    """Input arguments expected to run TRF."""
+
+    masked_genome_file = argschema.fields.InputFile(
+        required=True, description="Masked genome file path"
+    )
+    output_dir = argschema.fields.OutputDir(
+        required=True, description="Output directory path"
+    )
+    protein_file = argschema.fields.String(
+        required=True, description="Path for the protein dataset"
+    )
+    genblast_timeout_secs = argschema.fields.Integer(
+        required=False, default=10800, description="Genblast timeout period"
+    )
+    max_intron_length = argschema.fields.Integer(
+        required=True, description="Maximum intron length"
+    )
+    genblast_bin = argschema.fields.String(
+        required=False,
+        default="genblast",
+        description="Genblast executable path",
+    )
+    convert2blastmask_bin = argschema.fields.String(
+        required=False,
+        default="convert2blastmask",
+        description="convert2blastmask executable path",
+    )
+    makeblastdb_bin = argschema.fields.String(
+        required=False, default="makeblastdb", description="makeblastdb  executable path"
+    )
+    num_threads = argschema.fields.Integer(
+        required=False, default=1, description="Number of threads"
+    )
+    protein_set = argschema.fields.String(
+        required=True,
+        description="Protein set [uniprot,orthodb]",
+        validate=lambda x: x in ["uniprot", "orthodb"],
+    )
+
+
+def main() -> None:
+    """Genblast's entry-point."""
+    mod = argschema.ArgSchemaParser(schema_type=InputSchema)
+    log_file_path = create_dir(mod.args["output_dir"], "log") / "genblast.log"
+    loginipath = Path(__file__).parents[6] / "conf" / "logging.conf"
+    logging.config.fileConfig(
+        loginipath,
+        defaults={"logfilename": str(log_file_path)},
+        disable_existing_loggers=False,
+    )
+    run_genblast(
+        Path(mod.args["masked_genome_file"]),
+        Path(mod.args["output_dir"]),
+        Path(mod.args["protein_file"]),
+        mod.args["max_intron_length"],
+        mod.args["genblast_timeout_secs"],
+        Path(mod.args["genblast_bin"]),
+        Path(mod.args["convert2blastmask_bin"]),
+        Path(mod.args["makeblastdb_bin"]),
+        mod.args["num_threads"],
+        mod.args["protein_set"],
+    )
+
+
+if __name__ == "__main__":
+    main()
+
+ +
+
+
+
+
+
+ +

Table of Contents

+

Index

+ + +
+

Search

+
+ + +
+
+ +
+
+
+
+ +
+
+
+
+ modules | + index +
+
+
+
+ +
+ + +
+
+
+
+ + + \ No newline at end of file diff --git a/_modules/ensembl/tools/anno/repeat_annotation/dust.html b/_modules/ensembl/tools/anno/repeat_annotation/dust.html new file mode 100644 index 0000000..cc62410 --- /dev/null +++ b/_modules/ensembl/tools/anno/repeat_annotation/dust.html @@ -0,0 +1,306 @@ + + + + + + + ensembl.tools.anno.repeat_annotation.dust — ensembl-anno 0.1 documentation + + + + + + + + + + + +
+
+
+ +
+
+
+ +

Source code for ensembl.tools.anno.repeat_annotation.dust

+# See the NOTICE file distributed with this work for additional information #pylint: disable=missing-module-docstring
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""
+DustMasker is a program that identifies and masks out low complexity
+parts of a genome using a new and improved DUST algorithm.
+
+Morgulis A, Gertz EM, Schaffer AA, Agarwala R. A Fast and Symmetric
+DUST Implementation to Mask Low-Complexity DNA Sequences.
+"""
+__all__ = ["run_dust"]
+
+import logging
+import logging.config
+import multiprocessing
+import os
+from os import PathLike
+from pathlib import Path
+import re
+import subprocess
+import tempfile
+from typing import List
+import argschema
+
+
+from ensembl.tools.anno.utils._utils import (
+    check_exe,
+    create_dir,
+    check_gtf_content,
+    get_seq_region_length,
+    get_slice_id,
+    slice_output_to_gtf,
+    get_sequence,
+)
+
+logger = logging.getLogger(__name__)
+
+
+
[docs]def run_dust(
+    genome_file: PathLike,
+    output_dir: Path,
+    dust_bin: Path = Path("dustmasker"),
+    num_threads: int = 1,
+) -> None:
+    """
+    Run Dust on genomic slices with mutiprocessing
+        :param genome_file: Genome file path.
+        :type genome_file: PathLike
+        :param output_dir: Working directory path.
+        :type output_dir: Path
+        :param dust_bin: Dust software path.
+        :type dust_bin: Path, default dustmasker
+        :param num_threads: Number of threads.
+        :type num_threads: int, default 1
+                
+        :return: None
+        :rtype: None
+    """
+
+    check_exe(dust_bin)
+    dust_dir = create_dir(output_dir, "dust_output")
+    os.chdir(str(dust_dir))
+    output_file = dust_dir / "annotation.gtf"
+    if output_file.exists():
+        transcript_count = check_gtf_content(output_file, "repeat")
+        if transcript_count > 0:
+            logger.info("Dust gtf file exists, skipping analysis")
+            return
+    logger.info("Creating list of genomic slices")
+    seq_region_to_length = get_seq_region_length(genome_file, 5000)
+    slice_ids_per_region = get_slice_id(seq_region_to_length, slice_size=1000000, overlap=0, min_length=5000)
+    dust_cmd = [dust_bin, "-in"]
+    pool = multiprocessing.Pool(num_threads)  # pylint: disable=consider-using-with
+    for slice_id in slice_ids_per_region:
+        pool.apply_async(
+            _multiprocess_dust,
+            args=(
+                dust_cmd,
+                slice_id,
+                dust_dir,
+                genome_file,
+            ),
+        )
+    pool.close()
+    pool.join()
+    slice_output_to_gtf(dust_dir, "repeat_id", "dust", True, ".dust.gtf")
+    for gtf_file in dust_dir.glob("*.dust.gtf"):
+        gtf_file.unlink()

+
+
+def _multiprocess_dust(  # pylint: disable=too-many-locals
+    dust_cmd: List[str],
+    slice_id: List[str],
+    dust_dir: Path,
+    genome_file: Path,
+) -> None:
+    """
+    Run Dust on multiprocess on genomic slices
+    Args:
+        dust_cmd: Dust command to execute.
+        slice_id: List of slice IDs.
+        dust_dir : Dust output directory path.
+        genome_file : Genome file.
+    """
+    region_name, start, end = slice_id
+    logger.info(
+        "Processing slice to find low complexity regions with Dust: %s:%s:%s",
+        region_name,
+        start,
+        end,
+    )
+    seq = get_sequence(region_name, int(start), int(end), 1, genome_file, dust_dir)
+    slice_name = f"{region_name}.rs{start}.re{end}"
+    with tempfile.TemporaryDirectory(dir=dust_dir) as tmpdirname:
+        slice_file = dust_dir / tmpdirname / f"{slice_name}.fa"
+        with open(slice_file, "w+", encoding="utf8") as region_out:
+            region_out.write(f">{region_name}\n{seq}\n")
+        region_results = dust_dir / f"{slice_name}.dust.gtf"
+        output_file = Path(f"{slice_file}.dust")
+        dust_cmd.append(str(slice_file))
+        logger.info("dust_cmd: %s", dust_cmd)
+        with open(output_file, "w+", encoding="utf8") as dust_out:
+            subprocess.run(dust_cmd, stdout=dust_out, check=True)
+        _create_dust_gtf(output_file, region_results, region_name)
+        slice_file.unlink()
+        output_file.unlink()
+
+
+def _create_dust_gtf(
+    output_file: Path,
+    region_results: Path,
+    region_name: str,
+) -> None:
+    """
+    Read the fasta file and save the content in gtf format
+    All the genomic slices are collected in a single gtf output
+    Args:
+        output_file : GTF file with final results.
+        region_results : GTF file with the results per region.
+        region_name :Coordinates of genomic slice.
+    """
+    with open(output_file, "r", encoding="utf8") as dust_in, open(
+        region_results, "w+", encoding="utf8"
+    ) as dust_out:
+        repeat_count = 1
+        for line in dust_in:
+            result_match = re.search(r"(\d+)\ - (\d+)", line)
+            if result_match:
+                start = int(result_match.group(1)) + 1
+                end = int(result_match.group(2)) + 1
+                gtf_line = (
+                    f"{region_name}\tDust\trepeat\t{start}\t" f'{end}\t.\t+\t.\trepeat_id "{repeat_count}";\n'
+                )
+                dust_out.write(gtf_line)
+                repeat_count += 1
+
+
+class InputSchema(argschema.ArgSchema):
+    """Input arguments expected to run DustMasker."""
+
+    genome_file = argschema.fields.InputFile(required=True, description="Genome file path")
+    output_dir = argschema.fields.OutputDir(required=True, description="Output directory path")
+    dust_bin = argschema.fields.String(
+        required=False,
+        default="dustmasker",
+        description="Dust executable path",
+    )
+    num_threads = argschema.fields.Integer(required=False, default=1, description="Number of threads")
+
+
+def main() -> None:
+    """Dust's entry-point."""
+    mod = argschema.ArgSchemaParser(schema_type=InputSchema)
+    log_file_path = create_dir(mod.args["output_dir"], "log") / "dust.log"
+    loginipath = Path(__file__).parents[6] / "conf" / "logging.conf"
+    logging.config.fileConfig(
+        loginipath,
+        defaults={"logfilename": str(log_file_path)},
+        disable_existing_loggers=False,
+    )
+    run_dust(
+        mod.args["genome_file"],
+        mod.args["output_dir"],
+        mod.args["dust_bin"],
+        mod.args["num_threads"],
+    )
+
+
+if __name__ == "__main__":
+    main()
+
+ +
+
+
+
+
+
+ +

Table of Contents

+

Index

+ + +
+

Search

+
+ + +
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+
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+ modules | + index +
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+
+ + + \ No newline at end of file diff --git a/_modules/ensembl/tools/anno/repeat_annotation/red.html b/_modules/ensembl/tools/anno/repeat_annotation/red.html new file mode 100644 index 0000000..c010a31 --- /dev/null +++ b/_modules/ensembl/tools/anno/repeat_annotation/red.html @@ -0,0 +1,272 @@ + + + + + + + ensembl.tools.anno.repeat_annotation.red — ensembl-anno 0.1 documentation + + + + + + + + + + + +
+
+
+ +
+
+
+ +

Source code for ensembl.tools.anno.repeat_annotation.red

+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""
+Red is the first repeat-detection tool capable of labeling its training data
+and training itself automatically on an entire genome.
+Girgis, H.Z. Red: an intelligent, rapid, accurate tool for detecting repeats
+de-novo on the genomic scale. BMC Bioinformatics 16, 227 (2015).
+https://doi.org/10.1186/s12859-015-0654-5
+"""
+__all__ = ["run_red"]
+
+import logging
+import logging.config
+from os import PathLike
+from pathlib import Path
+import re
+import subprocess
+import argschema
+
+from ensembl.tools.anno.utils._utils import (
+    check_exe,
+    create_dir,
+)
+
+logger = logging.getLogger(__name__)
+
+
+
[docs]def run_red(genome_file: Path, output_dir: Path, red_bin: Path = Path("Red"),) -> str:
+    """
+    Run Red on genome file
+        :param genome_file: Genome file path.
+        :type genome_file: Path
+        :param output_dir: Working directory path.
+        :type output_dir: Path
+        :param red_bin: Red software path.
+        :type red_bin: Path, default Red
+        
+        :return: Masked genome file
+        :rtype: str
+    """
+    check_exe(red_bin)
+    red_dir = create_dir(output_dir, "red_output")
+    red_mask_dir = create_dir(red_dir, "mask_output")
+    red_repeat_dir = create_dir(red_dir, "repeat_output")
+    red_genome_dir = create_dir(red_dir, "genome_dir")
+
+    sym_link_genome_cmd = "ln -s " + str(genome_file) + " " + str(red_genome_dir)
+    genome_file_name = genome_file.name
+    red_genome_file = red_genome_dir / genome_file_name
+    genome_file_stem = genome_file.stem
+    masked_genome_file = red_mask_dir / f"{genome_file_stem}.msk"
+    repeat_coords_file = red_repeat_dir / f"{genome_file_stem}.rpt"
+    output_file = red_dir / "annotation.gtf"
+
+    if masked_genome_file.exists():
+        logger.warning(
+            "Masked Genome file already found on the path to the Red mask output dir. \
+            Will not create a new file"
+        )
+        # _create_red_gtf(repeat_coords_file, output_file)
+        return str(masked_genome_file)
+    if red_genome_file.exists():
+        logger.warning(
+            "Unmasked genome file already found on the path to the Red genome dir, \
+            will not create a sym link"
+        )
+
+    else:
+        logger.info(
+            "Preparing to sym link the genome file to the Red genome dir. Cmd\n %s",
+            sym_link_genome_cmd,
+        )
+        # subprocess.run(["ln", "-s", genome_file, red_genome_dir])
+        red_genome_file.symlink_to(genome_file)
+    try:
+        if red_genome_file.exists():
+         logger.info("Running Red")
+         subprocess.run(
+            [
+                red_bin,
+                "-gnm",
+                red_genome_dir,
+                "-msk",
+                red_mask_dir,
+                "-rpt",
+                red_repeat_dir,
+            ],
+            check=True,
+        )
+    except:
+        logger.error(
+            "Could not find the genome file in the Red genome dir or sym link \
+            to the original file. Path expected:\n%s",
+            genome_file,
+        )
+    _create_red_gtf(repeat_coords_file, output_file)
+    return str(masked_genome_file)

+
+
+def _create_red_gtf(repeat_coords_file: Path, output_file: Path):
+    """
+    Create Red gtf file from masked genome file
+
+    Args:
+        repeat_coords_file: Coordinates for repeats.
+        output_file : GTF file with the final results.
+    """
+    with open(repeat_coords_file, "r", encoding="utf8") as red_in, open(
+        output_file, "w+", encoding="utf8"
+    ) as red_out:
+        for repeat_id, line in enumerate(red_in, start=1):
+            result_match = re.search(r"^\>(.+)\:(\d+)\-(\d+)", line)
+            if result_match:
+                region_name = result_match.group(1)
+                # Note that Red is 0-based, so add 1
+                start = int(result_match.group(2)) + 1
+                end = int(result_match.group(3)) + 1
+                gtf_line = (
+                    f"{region_name}\tRed\trepeat\t{start}\t"
+                    f'{end}\t.\t+\t.\trepeat_id "{repeat_id}";\n'
+                )
+                red_out.write(gtf_line)
+
+
+class InputSchema(argschema.ArgSchema):
+    """Input arguments expected to run Red."""
+
+    genome_file = argschema.fields.InputFile(
+        required=True, description="Genome file path"
+    )
+    output_dir = argschema.fields.OutputDir(
+        required=True, description="Output directory path"
+    )
+    red_bin = argschema.fields.String(
+        required=False, default="Red", description="Red executable path",
+    )
+
+
+def main() -> None:
+    """Red's entry-point."""
+    mod = argschema.ArgSchemaParser(schema_type=InputSchema)
+    log_file_path = create_dir(mod.args["output_dir"], "log") / "red.log"
+    loginipath = Path(__file__).parents[6] / "conf" / "logging.conf"
+    logging.config.fileConfig(
+        loginipath,
+        defaults={"logfilename": str(log_file_path)},
+        disable_existing_loggers=False,
+    )
+    run_red(
+        Path(mod.args["genome_file"]), mod.args["output_dir"], mod.args["red_bin"],
+    )
+
+
+if __name__ == "__main__":
+    main()
+
+ +
+
+
+
+
+
+ +

Table of Contents

+

Index

+ + +
+

Search

+
+ + +
+
+ +
+
+
+
+ +
+
+
+
+ modules | + index +
+
+
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+ +
+ + +
+
+
+
+ + + \ No newline at end of file diff --git a/_modules/ensembl/tools/anno/repeat_annotation/repeatmasker.html b/_modules/ensembl/tools/anno/repeat_annotation/repeatmasker.html new file mode 100644 index 0000000..f086cc4 --- /dev/null +++ b/_modules/ensembl/tools/anno/repeat_annotation/repeatmasker.html @@ -0,0 +1,378 @@ + + + + + + + ensembl.tools.anno.repeat_annotation.repeatmasker — ensembl-anno 0.1 documentation + + + + + + + + + + + +
+
+
+ +
+
+
+ +

Source code for ensembl.tools.anno.repeat_annotation.repeatmasker

+# See the NOTICE file distributed with this work for additional information #pylint: disable=missing-module-docstring
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""
+    RepeatMasker is a program that screens DNA sequences for interspersed
+    repeats and low complexity DNA sequences.
+    Smit, AFA, Hubley, R & Green, P. RepeatMasker Open-4.0
+"""
+
+__all__ = ["run_repeatmasker"]
+
+import json
+import logging
+import logging.config
+import multiprocessing
+import os
+from os import PathLike
+from pathlib import Path
+import re
+import subprocess
+from typing import List
+import argschema
+
+from ensembl.tools.anno.utils._utils import (
+    check_exe,
+    create_dir,
+    check_gtf_content,
+    get_seq_region_length,
+    get_slice_id,
+    slice_output_to_gtf,
+    get_sequence,
+)
+logger = logging.getLogger('__name__')
+
+
+
[docs]def run_repeatmasker(
+    genome_file: PathLike,
+    output_dir: Path,
+    repeatmasker_bin: Path = Path("RepeatMasker"),
+    library: str = "",
+    repeatmasker_engine: str = "rmblast",
+    species: str = "",
+    num_threads: int = 1,
+) -> None:
+
+    """
+    Executes RepeatMasker on the genome slices and stores the final annotation.gtf in repeatmasker_output
+
+        :param genome_file: Genome file path.
+        :type genome_file: PathLike
+        :param output_dir: Output directory path.
+        :type output_dir: Path
+        :param repeatmasker_bin: RepeatMasker executable path.
+        :type repeatmasker_bin: Path, default RepeatMasker
+        :param library: Custom repeat library.
+        :type library: str
+        :param repeatmasker_engine: RepeatMasker engine.
+        :type repeatmasker_engine: str, default rmblast
+        :param species: Species name.
+        :type species: str
+        :param num_threads: Number of threads.
+        :type num_threads: int, default 1
+        
+        :return: None
+        :rtype: None
+    """
+    check_exe(repeatmasker_bin)
+    repeatmasker_dir = create_dir(output_dir, "repeatmasker_output")
+
+    output_file = repeatmasker_dir / "annotation.gtf"
+    if output_file.exists():
+        transcript_count = check_gtf_content(output_file, "repeat")
+        if transcript_count > 0:
+            logger.info("Repeatmasker gtf file exists")
+            return
+    logger.info("Creating list of genomic slices")
+    seq_region_to_length = get_seq_region_length(genome_file, 5000)
+    slice_ids_per_region = get_slice_id(
+        seq_region_to_length, slice_size=1000000, overlap=0, min_length=5000
+    )
+    repeatmasker_cmd = [
+        str(repeatmasker_bin),
+        "-nolow",#does not display simple repeats or low_complexity DNA in the annotation
+        "-engine",
+        repeatmasker_engine,
+        "-dir",
+        str(repeatmasker_dir),
+    ]
+    if not library:
+        if not species:
+            species = "homo"
+        repeatmasker_cmd.extend(["-species", species])
+    else:
+        repeatmasker_cmd.extend(["-lib", library])
+    logger.info(f"Running RepeatMasker {repeatmasker_cmd}")
+    pool = multiprocessing.Pool(num_threads)  # pylint: disable=consider-using-with
+    for slice_id in slice_ids_per_region:
+        pool.apply_async(
+            _multiprocess_repeatmasker,
+            args=(
+                repeatmasker_cmd,
+                slice_id,
+                genome_file,
+                repeatmasker_dir,
+            ),
+        )
+    pool.close()
+    pool.join()
+    slice_output_to_gtf(repeatmasker_dir, "repeat_id", "repeatmask", True, ".rm.gtf")
+    for gtf_file in repeatmasker_dir.glob("*.rm.gtf"):
+        gtf_file.unlink()

+
+def _multiprocess_repeatmasker(  # pylint: disable=too-many-locals
+    repeatmasker_cmd: List[str],
+    slice_id: List[str],
+    genome_file: Path,
+    repeatmasker_dir: Path,
+) -> None:
+    """
+    Run Repeatmasker on genomic slice
+
+    Args:
+        repeatmasker_cmd: RepeatMasker command to execute.
+        slice_id: Slice ID to run RepeatMasker on.
+        genome_file : Genome file path.
+        repeatmasker_dir : RepeatMasker output directory path.
+    """
+
+    region_name, start, end = slice_id
+    logger.info(
+        "Processing slice to find repeats with RepeatMasker: %s:%s:%s",
+        region_name,
+        start,
+        end,
+    )
+    seq = get_sequence(
+        region_name, int(start), int(end), 1, genome_file, repeatmasker_dir
+    )
+    slice_file_name = f"{region_name}.rs{start}.re{end}"
+    region_file = repeatmasker_dir / f"{slice_file_name}.fa"
+    with open(region_file, "w+", encoding="utf8") as region_fasta_out:
+        region_fasta_out.write(f">{region_name}\n{seq}\n")
+    region_results_file = Path(f"{region_file}.rm.gtf")
+    output_file = Path(f"{region_file}.out")
+    masked_file = Path(f"{region_file}.masked")
+    tbl_file = Path(f"{region_file}.tbl")
+    log_file = Path(f"{region_file}.log")
+    cat_file = Path(f"{region_file}.cat")
+    repeatmasker_cmd = repeatmasker_cmd.copy()
+    repeatmasker_cmd.append(str(region_file))
+    logger.info(repeatmasker_cmd)
+    subprocess.run(repeatmasker_cmd, check=True)
+    _create_repeatmasker_gtf(output_file, region_results_file, region_name)
+    output_file.unlink()
+    region_file.unlink()
+    masked_file.unlink(missing_ok=True)
+    tbl_file.unlink(missing_ok=True)
+    log_file.unlink(missing_ok=True)
+    cat_file.unlink(missing_ok=True)
+
+
+def _create_repeatmasker_gtf(  # pylint: disable=too-many-locals
+    output_file: Path,
+    region_results_file: Path,
+    region_name: str,
+) -> None:
+    """
+    Read the fasta file and save the content in gtf format
+
+    All the genomic slices are collected in a single gtf output with the following format:
+    SW    perc perc perc query    position in query matching repeat       position in repeat
+    score div. del. ins. sequence begin end (left)  repeat   class/family begin end  (left)  ID
+    Args:
+        output_file : GTF file with final results.
+        region_results_file_path : GTF file with results per region.
+        region_name : Coordinates of genomic slice.
+    """
+    with open(output_file, "r", encoding="utf8") as repeatmasker_in, open(
+        region_results_file, "w+", encoding="utf8"
+    ) as repeatmasker_out:
+        repeat_count = 1
+        for line in repeatmasker_in:
+            result_match = re.search(r"^\s*\d+\s+", line)
+            if result_match:
+                results = line.split()
+                if results[-1] == "*":
+                    results.pop()
+                if len(results) != 15:
+                    continue
+                score = results[0]
+                start = results[5]
+                end = results[6]
+                strand = results[8]
+                repeat_name = results[9]
+                repeat_class = results[10]
+                if strand == "+":
+                    repeat_start = results[11]
+                    repeat_end = results[12]
+                else:
+                    repeat_start = results[13]
+                    repeat_end = results[12]
+                    strand = "-"
+                gtf_line = (
+                    f"{region_name}\tRepeatMasker\trepeat\t{start}\t{end}\t.\t"
+                    f"{strand}\t.\trepeat_id{repeat_count}; "
+                    f'repeat_name "{repeat_name}"; repeat_class "{repeat_class}"; '
+                    f'repeat_start "{repeat_start}"; '
+                    f'repeat_end "{repeat_end}"; score "{score}";\n'
+                )
+                repeatmasker_out.write(gtf_line)
+                repeat_count += 1
+
+
+class InputSchema(argschema.ArgSchema):
+    """Input arguments expected to run RepeatMasker."""
+
+    genome_file = argschema.fields.InputFile(
+        required= True, description= "Genome file path"
+    )
+    output_dir = argschema.fields.OutputDir(
+        required= True, description= "Output directory path"
+    )
+    repeatmasker_bin = argschema.fields.String(
+        required= False, default= "RepeatMasker",
+            description = "RepeatMasker executable path",
+
+    )
+    library = argschema.fields.String(
+            required= False, default= "", description= "Custom repeat library"
+    )
+    repeatmasker_engine = argschema.fields.String(
+            required= False, default= "rmblast", description= "RepeatMasker engine"
+    )
+    species = argschema.fields.String(
+            required= False,
+            default="homo",
+            description="Species name (used if no library is provided)"
+    )
+    num_threads = argschema.fields.Integer(
+            required= False, default= 1, description= "Number of threads"
+    )
+
+
+def main() -> None:
+    """RepeatMasker's entry-point."""
+    mod = argschema.ArgSchemaParser(schema_type=InputSchema)
+    log_file_path = create_dir(mod.args["output_dir"], "log") /"repeatmasking.log"
+    loginipath = Path(__file__).parents[6] / "conf" / "logging.conf"
+    logging.config.fileConfig(loginipath, defaults={"logfilename": str(log_file_path)}, disable_existing_loggers=False,)
+    run_repeatmasker(
+        mod.args["genome_file"],
+        mod.args["output_dir"],
+        mod.args["repeatmasker_bin"],
+        mod.args["library"],
+        mod.args["repeatmasker_engine"],
+        mod.args["species"],
+        mod.args["num_threads"],
+        )
+
+if __name__ == "__main__":
+    main()
+
+
+ +
+
+
+
+
+
+ +

Table of Contents

+

Index

+ + +
+

Search

+
+ + +
+
+ +
+
+
+
+ +
+
+
+
+ modules | + index +
+
+
+
+ +
+ + +
+
+
+
+ + + \ No newline at end of file diff --git a/_modules/ensembl/tools/anno/repeat_annotation/trf.html b/_modules/ensembl/tools/anno/repeat_annotation/trf.html new file mode 100644 index 0000000..504bb56 --- /dev/null +++ b/_modules/ensembl/tools/anno/repeat_annotation/trf.html @@ -0,0 +1,410 @@ + + + + + + + ensembl.tools.anno.repeat_annotation.trf — ensembl-anno 0.1 documentation + + + + + + + + + + + +
+
+
+ +
+
+
+ +

Source code for ensembl.tools.anno.repeat_annotation.trf

+# See the NOTICE file distributed with this work for additional information #pylint: disable=missing-module-docstring
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""
+    Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.
+    Benson G. Tandem repeats finder: a program to analyze DNA sequences.
+    Nucleic Acids Res. 1999; 27(2):573–580. doi:10.1093/nar/27.2.573
+"""
+__all__ = ["run_trf"]
+
+import logging
+import logging.config
+import multiprocessing
+import os
+from os import PathLike
+from pathlib import Path
+import re
+import subprocess
+import tempfile
+from typing import List
+import argschema
+
+from ensembl.tools.anno.utils._utils import (
+    check_exe,
+    create_dir,
+    check_gtf_content,
+    get_seq_region_length,
+    get_slice_id,
+    slice_output_to_gtf,
+    get_sequence,
+)
+
+logger = logging.getLogger(__name__)
+
+
+
[docs]def run_trf(
+    genome_file: PathLike,
+    output_dir: Path,
+    num_threads: int = 1,
+    trf_bin: Path = Path("trf"),
+    match_score: int = 2,
+    mismatch_score: int = 5,
+    delta: int = 7,
+    pm: int = 80,
+    pi: int = 10,
+    minscore: int = 40,
+    maxperiod: int = 500,
+) -> None:
+    """
+    Executes TRF on genomic slices
+            :param genome_file: Genome file path.
+            :type genome_file: PathLike
+            :param output_dir:  Working directory path.
+            :type output_dir: Path
+            :param num_threads: int, number of threads.
+            :type num_threads: int, default 1
+            :param trf_bin: TRF software path.
+            :type trf_bin: Path, default trf
+            :param match_score: Matching weight.
+            :type match_score: int, default 2
+            :param mismatch_score: Mismatching penalty.
+            :type mismatch_score: int, default 5
+            :param delta: Indel penalty.
+            :type delta: int, default 7
+            :param pm: Match probability (whole number).
+            :type pm: int, default 80
+            :param pi: Indel probability (whole number).
+            :type pi: int, default 10
+            :param minscore: Minimum alignment score to report.
+            :type minscore: int, default 40
+            :param maxperiod: Maximum period size to report.
+            :type maxperiod: int, default 500
+                    
+            :return: None
+            :rtype: None
+    """
+    check_exe(trf_bin)
+    trf_dir = create_dir(output_dir, "trf_output")
+    os.chdir(str(trf_dir))
+    output_file = trf_dir / "annotation.gtf"
+    if output_file.exists():
+        transcript_count = check_gtf_content(output_file, "repeat")
+        if transcript_count > 0:
+            logger.info("Trf gtf file exists, skipping analysis")
+            return
+    logger.info("Creating list of genomic slices")
+    seq_region_to_length = get_seq_region_length(genome_file, 5000)
+    slice_ids_per_region = get_slice_id(
+        seq_region_to_length, slice_size=1000000, overlap=0, min_length=5000
+    )
+    trf_output_extension = (
+        f".{match_score}.{mismatch_score}.{delta}."
+        f"{pm}.{pi}.{minscore}.{maxperiod}.dat"
+    )
+    trf_cmd = [
+        trf_bin,
+        None,
+        str(match_score),
+        str(mismatch_score),
+        str(delta),
+        str(pm),
+        str(pi),
+        str(minscore),
+        str(maxperiod),
+        "-d",
+        "-h",
+    ]
+    logger.info("Running TRF")
+    pool = multiprocessing.Pool(num_threads)#pylint:disable=consider-using-with
+    for slice_id in slice_ids_per_region:
+        pool.apply_async(
+            _multiprocess_trf,
+            args=(
+                trf_cmd,
+                slice_id,
+                trf_dir,
+                trf_output_extension,
+                genome_file,
+            ),
+        )
+    pool.close()
+    pool.join()
+    slice_output_to_gtf(trf_dir, "repeat_id", "trf", True, ".trf.gtf")
+    for gtf_file in trf_dir.glob("*.trf.gtf"):
+        gtf_file.unlink()

+
+
+def _multiprocess_trf(
+    trf_cmd: List[str],
+    slice_id: List[str],
+    trf_dir: Path,
+    trf_output_extension: Path,
+    genome_file:Path,
+) -> None:
+    """
+    Run TRF on multiprocess on genomic slices
+    Args:
+        trf_cmd: TRF command to execute.
+        slice_id: Slice Id to run TRF on.
+        trf_dir : TRF output dir.
+        trf_output_extension: TRF file output extension.
+        genome_file : Genome file.
+    """
+    region_name, start, end = slice_id
+    logger.info(
+        "Processing slice to find tandem repeats with TRF:%s:%s:%s",
+        region_name,
+        start,
+        end,
+    )
+    seq = get_sequence(region_name, int(start), int(end), 1, genome_file, trf_dir)
+    slice_name = f"{region_name}.rs{start}.re{end}"
+    with tempfile.TemporaryDirectory(dir=trf_dir) as tmpdirname:
+        slice_file = trf_dir / tmpdirname / f"{slice_name}.fa"
+        with open(slice_file, "w+", encoding="utf8") as region_out:
+            region_out.write(f">{region_name}\n{seq}\n")
+        region_results = trf_dir / f"{slice_name}.trf.gtf"
+        # TRF writes to the current dir, so swtich to the output dir for it
+        # os.chdir(str(trf_output_dir))
+        output_file = Path(f"{slice_file}{trf_output_extension}")
+        trf_cmd = trf_cmd.copy()
+        trf_cmd[1] = str(slice_file)
+        logger.info("trf_cmd: %s", trf_cmd)
+        # with open(trf_output_file_path, "w+") as trf_out:
+        subprocess.run(trf_cmd, cwd=trf_dir / tmpdirname)#pylint:disable=subprocess-run-check
+        _create_trf_gtf(output_file, region_results, region_name)
+        slice_file.unlink()
+        output_file.unlink()
+
+
+def _create_trf_gtf(
+    output_file: Path,
+    region_results: Path,
+    region_name: str,
+) -> None:
+    """
+    Read the fasta file and save the content in gtf format
+
+    TRF output format:
+    cols 1+2:  Indices of the repeat relative to the start of the sequence
+    col 3:     Period size of the repeat
+    col 4:     Number of copies aligned with the consensus pattern
+    col 5:     Size of consensus pattern (may differ slightly from the period size)
+    col 6:     Percent of matches between adjacent copies overall
+    col 7:     Percent of indels between adjacent copies overall
+    col 8:     Alignment score
+    cols 9-12: Percent composition for each of the four nucleotides
+    col 13:    Entropy measure based on percent composition
+    col 14:    Consensus sequence
+    col 15:    Repeat sequence
+    Args:
+       output_file : GTF file with final results.
+       region_results : GTF file with results per region.
+       region_name : Coordinates of genomic slice.
+    """
+    with open(output_file, "r", encoding="utf8") as trf_in, open(
+        region_results, "w+", encoding="utf8"
+    ) as trf_out:
+        repeat_count = 1
+        for line in trf_in:
+            result_match = re.search(r"^\d+", line)
+            if result_match:
+                results = line.split()
+                if len(results) != 15:
+                    continue
+                start = results[0]
+                end = results[1]
+                period = float(results[2])
+                copy_number = float(results[3])
+                percent_matches = float(results[5])
+                score = float(results[7])
+                repeat_consensus = results[13]
+                if (  # pylint: disable=too-many-boolean-expressions
+                    score < 50
+                    and percent_matches >= 80
+                    and copy_number > 2
+                    and period < 10
+                ) or (copy_number >= 2 and percent_matches >= 70 and score >= 50):
+                    gtf_line = (
+                        f"{region_name}\tTRF\trepeat\t{start}\t{end}\t.\t+\t.\t"
+                        f'repeat_id "{repeat_count}"; score "{score}"; '
+                        f'repeat_consensus "{repeat_consensus}";\n'
+                    )
+                    trf_out.write(gtf_line)
+                    repeat_count += 1
+
+
+class InputSchema(argschema.ArgSchema):
+    """Input arguments expected to run TRF."""
+
+    genome_file = argschema.fields.InputFile(
+        required=True, description="Genome file path"
+    )
+    output_dir = argschema.fields.OutputDir(
+        required=True, description="Output directory path"
+    )
+    trf_bin = argschema.fields.String(
+        required=False,
+        default="trf",
+        description="TRF executable path",
+    )
+    match_score = argschema.fields.Integer(
+        required=False, default=2, description="Matching weight"
+    )
+    mismatch_score = argschema.fields.Integer(
+        required=False, default=5, description="Mismatching penalty"
+    )
+    delta = argschema.fields.Integer(
+        required=False, default=7, description="Indel penalty"
+    )
+    pm = argschema.fields.Integer(
+        required=False, default=80, description="Match probability"
+    )
+    pi = argschema.fields.Integer(
+        required=False, default=10, description="Indel probability"
+    )
+    minscore = argschema.fields.Integer(
+        required=False, default=40, description="Minimum alignment score to report"
+    )
+    maxperiod = argschema.fields.Integer(
+        required=False, default=500, description="Maximum period size to report"
+    )
+    num_threads = argschema.fields.Integer(
+        required=False, default=1, description="Number of threads"
+    )
+
+
+def main() -> None:
+    """TRF's entry-point."""
+    mod = argschema.ArgSchemaParser(schema_type=InputSchema)
+    log_file_path = create_dir(mod.args["output_dir"], "log") / "trf.log"
+    loginipath = Path(__file__).parents[6] / "conf" / "logging.conf"
+    logging.config.fileConfig(
+        loginipath,
+        defaults={"logfilename": str(log_file_path)},
+        disable_existing_loggers=False,
+    )
+    run_trf(
+        mod.args["genome_file"],
+        mod.args["output_dir"],
+        mod.args["num_threads"],
+        mod.args["trf_bin"],
+        mod.args["match_score"],
+        mod.args["mismatch_score"],
+        mod.args["delta"],
+        mod.args["pm"],
+        mod.args["pi"],
+        mod.args["minscore"],
+        mod.args["maxperiod"],
+    )
+
+
+if __name__ == "__main__":
+    main()
+
+ +
+
+
+
+
+
+ +

Table of Contents

+

Index

+ + +
+

Search

+
+ + +
+
+ +
+
+
+
+ +
+
+
+
+ modules | + index +
+
+
+
+ +
+ + +
+
+
+
+ + + \ No newline at end of file diff --git a/_modules/ensembl/tools/anno/simple_feature_annotation/cpg.html b/_modules/ensembl/tools/anno/simple_feature_annotation/cpg.html new file mode 100644 index 0000000..28c5c2f --- /dev/null +++ b/_modules/ensembl/tools/anno/simple_feature_annotation/cpg.html @@ -0,0 +1,369 @@ + + + + + + + ensembl.tools.anno.simple_feature_annotation.cpg — ensembl-anno 0.1 documentation + + + + + + + + + + + +
+
+
+ +
+
+
+ +

Source code for ensembl.tools.anno.simple_feature_annotation.cpg

+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""
+Set of discriminant functions that can recognize structural and compositional features
+such as CpG islands, promoter regions and first splice-donor sites.
+Davuluri RV, Grosse I, Zhang MQ: Computational identification of promoters and
+first exons in the human genome. Nat Genet. 2001, 29(4):412-417. [PMID: 11726928]
+"""
+__all__ = ["run_cpg"]
+import logging
+import logging.config
+import multiprocessing
+from os import PathLike
+from pathlib import Path
+import re
+import subprocess
+from tempfile import TemporaryDirectory
+from typing import List,Union
+import argschema
+
+from ensembl.tools.anno.utils._utils import (
+    check_exe,
+    create_dir,
+    check_gtf_content,
+    get_seq_region_length,
+    get_slice_id,
+    slice_output_to_gtf,
+    get_sequence,
+)
+
+logger = logging.getLogger(__name__)
+
+
+
[docs]def run_cpg(
+    genome_file: PathLike,
+    output_dir: Path,
+    cpg_bin: Path = Path("cpg_lh"),
+    cpg_min_length: int = 400,
+    cpg_min_gc_content: int = 50,
+    cpg_min_oe: float = 0.6,
+    num_threads: int = 1,
+) -> None:
+    """
+    Run CpG islands on genomic slices
+
+        :param genome_file: Genome file path.
+        :type genome_file: PathLike
+        :param output_dir: Working directory path
+        :type output_dir: Path
+        :param cpg_bin: CpG software path.
+        :type cpg_bin: Path
+        :param cpg_min_length: Min length of CpG islands
+        :type cpg_min_length: int
+        :param cpg_min_gc_content: Min GC frequency percentage
+        :type cpg_min_gc_content: int
+        :param cpg_min_oe:  Min ratio of the observed to expected number of CpG (CpGo/e)
+        :type cpg_min_oe: float
+        :param num_threads: int, number of threads.
+        :type num_threads: int
+        
+        :return: None
+        :rtype: None
+    """
+
+    check_exe(cpg_bin)
+    cpg_dir = create_dir(output_dir, "cpg_output")
+    output_file = cpg_dir / "annotation.gtf"
+    if output_file.exists():
+        transcript_count = check_gtf_content(output_file, "simple_feature")
+        if transcript_count > 0:
+            logger.info("Cpg gtf file exists")
+            return
+    logger.info("Creating list of genomic slices")
+    seq_region_to_length = get_seq_region_length(genome_file, 5000)
+    slice_ids_per_region = get_slice_id(
+        seq_region_to_length, slice_size=1000000, overlap=0, min_length=5000
+    )
+    logger.info("Running CpG")
+    pool = multiprocessing.Pool(int(num_threads))  # pylint:disable=consider-using-with
+    for slice_id in slice_ids_per_region:
+        pool.apply_async(
+            _multiprocess_cpg,
+            args=(
+                cpg_bin,
+                slice_id,
+                genome_file,
+                cpg_dir,
+                cpg_min_length,
+                cpg_min_gc_content,
+                cpg_min_oe,
+            ),
+        )
+
+    pool.close()
+    pool.join()
+    slice_output_to_gtf(cpg_dir, "feature_id", "cpg", True, ".cpg.gtf")
+    for gtf_file in cpg_dir.glob("*.cpg.gtf"):
+        gtf_file.unlink()

+
+
+def _multiprocess_cpg(
+    cpg_bin: Path,
+    slice_id: List[str],
+    genome_file: Path,
+    cpg_dir: Path,
+    cpg_min_length: int = 400,
+    cpg_min_gc_content: int = 50,
+    cpg_min_oe: float = 0.6,
+) -> None:
+    """
+    Annotation of CpG islands on multiprocess on genomic slices
+    Args:
+        cpg_bin: CpG software path.
+        slice_id: Slice id to run CpG on.
+        genome_file : Genome file.
+        cpg_dir : Output dir.
+        cpg_min_length : Min length of CpG islands
+        cpg_min_gc_content : Min GC frequency percentage
+        cpg_min_oe :  Min ratio of the observed to expected number of CpG (CpGo/e)
+    """
+    region_name, start, end = slice_id
+    logger.info(
+        "Processing slice to find CpG islands with cpg_lh: %s:%s:%s",
+        region_name,
+        start,
+        end,
+    )
+    seq = get_sequence(region_name, int(start), int(end), 1, genome_file, cpg_dir)
+    slice_name = f"{region_name}.rs{start}.re{end}"
+    #with TemporaryDirectory(dir=cpg_dir) as tmpdirname:
+    slice_file = cpg_dir / f"{slice_name}.fa"
+    with open(slice_file, "w+", encoding="utf8") as region_out:
+        region_out.write(f">{region_name}\n{seq}\n")
+    region_results = cpg_dir / f"{slice_file}.cpg.gtf"
+    output_file = Path(f"{slice_file}.cpg")
+    cpg_cmd = [str(cpg_bin), str(slice_file)]
+    with open(output_file, "w+", encoding="utf8") as cpg_out:
+        subprocess.run(cpg_cmd, stdout=cpg_out, check=True)
+        _create_cpg_gtf(
+            output_file,
+            region_results,
+            region_name,
+            cpg_min_length,
+            cpg_min_gc_content,
+            cpg_min_oe,
+        )
+    slice_file.unlink()
+    output_file.unlink()
+
+
+def _create_cpg_gtf(
+    output_file: Path,
+    region_results: Path,
+    region_name: str,
+    cpg_min_length: int = 400,
+    cpg_min_gc_content: int = 50,
+    cpg_min_oe: float = 0.6,
+) -> None:
+    """
+    Read the fasta file and save the content in gtf format
+    All the genomic slices are collected in a single gtf output
+    Args:
+        output_file : GTF file with final results.
+        region_results : GTF file with the results per region.
+        region_name :Coordinates of genomic slice.
+        cpg_dir : Output dir.
+        cpg_min_length : Min length of CpG islands
+        cpg_min_gc_content : Min GC frequency percentage
+        cpg_min_oe :  Min ratio of the observed to expected number of CpG (CpGo/e)
+    """
+    with open(output_file, "r", encoding="utf8") as cpg_in, open(region_results, "w+", encoding="utf8") as cpg_out:
+        feature_count = 1
+        for line in cpg_in:
+            result_match = re.search(r"^" + region_name, line)
+            if result_match:
+                results = line.split()
+                start = int(results[1])
+                end = int(results[2])
+                length = end - start + 1
+                score = float(results[3])
+                gc_content = float(results[6])
+                oe_score_str = results[7]
+                oe_score: Union[float, int]
+                if oe_score_str in ("-", "inf"):
+                    oe_score=0
+                else:
+                    oe_score=float(oe_score_str)
+                if (
+                    int(length) >= int(cpg_min_length)
+                    and gc_content >= int(cpg_min_gc_content)
+                    and oe_score >= float(cpg_min_oe)
+                ):
+                    gtf_line = (
+                        f"{region_name}\tCpG\tsimple_feature\t{start}\t"
+                        f'{end}\t.\t+\t.\tfeature_id "{feature_count}"; score "{score}";\n'
+                    )
+                    cpg_out.write(gtf_line)
+
+
+class InputSchema(argschema.ArgSchema):
+    """Input arguments expected to run CpG software."""
+
+    genome_file = argschema.fields.InputFile(
+        required=True, description="Genome file path"
+    )
+    output_dir = argschema.fields.OutputDir(
+        required=True, description="Output directory path"
+    )
+    cpg_bin = argschema.fields.String(
+        required=False,
+        default="cpg_lh",
+        description="CpG executable path",
+    )
+    cpg_min_length = argschema.fields.Integer(
+        required=False,
+        default="400",
+        description="Min length of CpG islands",
+    )
+    cpg_min_gc_content = argschema.fields.Integer(
+        required=False,
+        default="50",
+        description="Min GC frequency percentage",
+    )
+    cpg_min_oe = argschema.fields.Float(
+        required=False,
+        default="0.6",
+        description="Min ratio of the observed to expected number of CpG (CpGo/e)",
+    )
+    num_threads = argschema.fields.Integer(
+        required=False, default=1, description="Number of threads"
+    )
+
+
+def main() -> None:
+    """CpG's entry-point."""
+    mod = argschema.ArgSchemaParser(schema_type=InputSchema)
+    log_file_path = create_dir(mod.args["output_dir"], "log") / "cpg.log"
+    loginipath = Path(__file__).parents[6] / "conf" / "logging.conf"
+    logging.config.fileConfig(
+        loginipath,
+        defaults={"logfilename": str(log_file_path)},
+        disable_existing_loggers=False,
+    )
+    run_cpg(
+        mod.args["genome_file"],
+        mod.args["output_dir"],
+        mod.args["cpg_bin"],
+        mod.args["cpg_min_length"],
+        mod.args["cpg_min_gc_content"],
+        mod.args["cpg_min_oe"],
+        mod.args["num_threads"],
+    )
+
+ +
+
+
+
+
+
+ +

Table of Contents

+

Index

+ + +
+

Search

+
+ + +
+
+ +
+
+
+
+ +
+
+
+
+ modules | + index +
+
+
+
+ +
+ + +
+
+
+
+ + + \ No newline at end of file diff --git a/_modules/ensembl/tools/anno/simple_feature_annotation/eponine.html b/_modules/ensembl/tools/anno/simple_feature_annotation/eponine.html new file mode 100644 index 0000000..4bb18bd --- /dev/null +++ b/_modules/ensembl/tools/anno/simple_feature_annotation/eponine.html @@ -0,0 +1,351 @@ + + + + + + + ensembl.tools.anno.simple_feature_annotation.eponine — ensembl-anno 0.1 documentation + + + + + + + + + + + +
+
+
+ +
+
+
+ +

Source code for ensembl.tools.anno.simple_feature_annotation.eponine

+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""
+Eponine is a probabilistic method for detecting transcription start sites (TSS)
+in mammalian genomic sequence, with good specificity and excellent positional accuracy.
+Down TA, Hubbard TJ. Computational detection and location of transcription start sites
+in mammalian genomic DNA. Genome Res. 2002 Mar;12(3):458-61. doi: 10.1101/gr.216102.
+PMID: 11875034; PMCID: PMC155284.
+"""
+__all__ = ["run_eponine"]
+
+import logging
+import logging.config
+import multiprocessing
+import os
+from os import PathLike
+from pathlib import Path
+import re
+import subprocess
+from tempfile import TemporaryDirectory
+from typing import List
+import argschema
+
+from ensembl.tools.anno.utils._utils import (
+    check_exe,
+    check_file,
+    create_dir,
+    check_gtf_content,
+    get_sequence,
+    get_seq_region_length,
+    get_slice_id,
+    slice_output_to_gtf,
+)
+
+logger = logging.getLogger("__name__")
+
+
+
[docs]def run_eponine(
+    genome_file: PathLike,
+    output_dir: Path,
+    num_threads: int = 1,
+    java_bin: Path = Path("java"),
+    eponine_bin: Path = Path(
+        "/hps/software/users/ensembl/ensw/C8-MAR21-sandybridge/linuxbrew/opt/eponine/libexec/eponine-scan.jar"
+    ),
+    eponine_threshold: float = 0.999,
+) -> None:
+    """
+    Run Eponine on genomic slices
+        :param genome_file: Genome file path.
+        :param genome_file: PathLike
+        :param output_dir: Working directory path.
+        :param output_dir: Path
+        :param java_bin: Java path.
+        :param java_bin: Path, default java
+        :param eponine_bin: Eponine software path
+        :param eponine_bin: Path
+        :param num_threads: Number of threads.
+        :param num_threads: int, default 1
+                        
+        :return: None
+        :rtype: None
+    """
+    check_file(eponine_bin)
+    check_exe(java_bin)
+    eponine_dir = create_dir(output_dir, "eponine_output")
+    # os.chdir(str(eponine_dir))
+    output_file = eponine_dir / "annotation.gtf"
+    if output_file.exists():
+        transcript_count = check_gtf_content(output_file, "simple_feature")
+        if transcript_count > 0:
+            logger.info("Eponine gtf file exists, skipping analysis")
+            return
+    logger.info("Creating list of genomic slices")
+    seq_region_to_length = get_seq_region_length(genome_file, 5000)
+    slice_ids_per_region = get_slice_id(
+        seq_region_to_length, slice_size=1000000, overlap=0, min_length=5000
+    )
+
+    eponine_cmd = [
+        str(java_bin),
+        "-jar",
+        str(eponine_bin),
+        "-threshold",
+        str(eponine_threshold),
+        "-seq",
+    ]
+    logger.info("Running Eponine")
+    pool = multiprocessing.Pool(int(num_threads))  # pylint:disable=consider-using-with
+    for slice_id in slice_ids_per_region:
+        pool.apply_async(
+            _multiprocess_eponine,
+            args=(
+                eponine_cmd,
+                slice_id,
+                eponine_dir,
+                Path(genome_file),
+            ),
+        )
+    pool.close()
+    pool.join()
+    slice_output_to_gtf(eponine_dir, "feature_id", "eponine", True, ".epo.gtf")
+    for gtf_file in eponine_dir.glob("*.epo.gtf"):
+        gtf_file.unlink()

+
+
+def _multiprocess_eponine(
+    eponine_cmd: List[str],
+    slice_id: List[str],
+    eponine_dir: Path,
+    genome_file: Path,
+) -> None:
+    """
+    Run Eponine on multiprocess on genomic slices
+    Args:
+        eponine_cmd: Eponine command to execute.
+        slice_id: List of slice IDs.
+        eponine_dir : Eponine output directory path.
+        genome_file : Genome file.
+    """
+    region_name, start, end = slice_id
+    logger.info(
+        "Processing slice to find transcription start sites with Eponine: %s:%s:%s",
+        region_name,
+        start,
+        end,
+    )
+    seq = get_sequence(region_name, int(start), int(end), 1, genome_file, eponine_dir)
+    slice_name = f"{region_name}.rs{start}.re{end}"
+    #with tempfile.TemporaryDirectory(dir=eponine_dir) as tmpdirname:
+    slice_file = eponine_dir / f"{slice_name}.fa"
+    with open(slice_file, "w+", encoding="utf8") as region_out:
+        region_out.write(f">{region_name}\n{seq}\n")
+    region_results = eponine_dir / f"{slice_name}.epo.gtf"
+    output_file = Path(f"{slice_file}.epo")
+    eponine_cmd = eponine_cmd.copy()
+    eponine_cmd.append(str(slice_file))
+    logging.info(eponine_cmd)
+    with open(output_file, "w+", encoding="utf8") as eponine_out:
+        subprocess.run(eponine_cmd, stdout=eponine_out, check=True)
+    _create_eponine_gtf(output_file, region_results, region_name)
+    slice_file.unlink()
+    output_file.unlink()
+
+
+def _create_eponine_gtf(
+    output_file: Path,
+    region_results: Path,
+    region_name: str,
+) -> None:
+    """
+    Read the fasta file and save the content in gtf format
+    All the genomic slices are collected in a single gtf output
+    Args:
+        output_file: GTF file with final results.
+        region_results: GTF file with the results per region.
+        region_name: Coordinates of genomic slice.
+    """
+    with open(output_file, "r", encoding="utf8") as eponine_in, open(
+        region_results, "w+", encoding="utf8"
+    ) as eponine_out:
+        feature_count = 1
+        for line in eponine_in:
+            result_match = re.search(r"^" + region_name, line)
+            if result_match:
+                results = line.split()
+                start = int(results[3])
+                end = int(results[4])
+                score = float(results[5])
+                strand = results[6]
+                logging.info(results)
+                # There's a one base offset on the reverse strand
+                if strand == "-":
+                    start -= 1
+                    end -= 1
+
+                gtf_line = (
+                    f"{region_name}\tEponine\tsimple_feature\t"
+                    f"{start}\t{end}\t.\t{strand}\t.\t"
+                    f'feature_id "{feature_count}"; score "{score}";\n'
+                )
+                eponine_out.write(gtf_line)
+                feature_count += 1
+
+
+class InputSchema(argschema.ArgSchema):
+    """Input arguments expected to run Eponine."""
+
+    genome_file = argschema.fields.InputFile(
+        required=True, description="Genome file path"
+    )
+    output_dir = argschema.fields.OutputDir(
+        required=True, description="Output directory path"
+    )
+    num_threads = argschema.fields.Integer(
+        required=False, default=1, description="Number of threads"
+    )
+    java_bin = argschema.fields.String(
+        required=False,
+        default="java",
+        description="Java executable path",
+    )
+    eponine_bin = argschema.fields.String(
+        required=False,
+        default="/hps/software/users/ensembl/ensw/C8-MAR21-sandybridge/linuxbrew/opt/eponine/libexec/eponine-scan.jar",  # pylint:disable=line-too-long
+        description="Java executable path",
+    )
+    eponine_threashold = argschema.fields.Float(
+        required=False, default=0.999, description="Eponine threashold"
+    )
+
+
+def main() -> None:
+    """Eponine's entry-point."""
+    mod = argschema.ArgSchemaParser(schema_type=InputSchema)
+    log_file_path = create_dir(mod.args["output_dir"], "log") / "eponine.log"
+    loginipath = Path(__file__).parents[6] / "conf" / "logging.conf"
+    logging.config.fileConfig(
+        loginipath,
+        defaults={"logfilename": str(log_file_path)},
+        disable_existing_loggers=False,
+    )
+    run_eponine(
+        mod.args["genome_file"],
+        mod.args["output_dir"],
+        mod.args["num_threads"],
+        Path(mod.args["java_bin"]),
+        Path(mod.args["eponine_bin"]),
+        mod.args["eponine_threashold"],
+    )
+
+
+if __name__ == "__main__":
+    main()
+
+ +
+
+
+
+
+
+ +

Table of Contents

+

Index

+ + +
+

Search

+
+ + +
+
+ +
+
+
+
+ +
+
+
+
+ modules | + index +
+
+
+
+ +
+ + +
+
+
+
+ + + \ No newline at end of file diff --git a/_modules/ensembl/tools/anno/snc_rna_annotation/trnascan.html b/_modules/ensembl/tools/anno/snc_rna_annotation/trnascan.html new file mode 100644 index 0000000..22caf86 --- /dev/null +++ b/_modules/ensembl/tools/anno/snc_rna_annotation/trnascan.html @@ -0,0 +1,405 @@ + + + + + + + ensembl.tools.anno.snc_rna_annotation.trnascan — ensembl-anno 0.1 documentation + + + + + + + + + + + +
+
+
+ +
+
+
+ +

Source code for ensembl.tools.anno.snc_rna_annotation.trnascan

+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""
+tRNAscan-SE identifies 99-100% of transfer RNA genes in DNA sequence while
+giving less than one false positive per 15 gigabases.
+Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer
+RNA genes in genomic sequence.
+Nucleic Acids Res. 1997, 25(5):955-64. [PMID: 9023104]
+"""
+__all__ = ["run_trnascan"]
+
+import logging
+import logging.config
+import multiprocessing
+from os import PathLike
+from pathlib import Path
+import re
+import subprocess
+from typing import List
+import argschema
+
+from ensembl.tools.anno.utils._utils import (
+    check_exe,
+    check_file,
+    create_dir,
+    check_gtf_content,
+    get_seq_region_length,
+    get_slice_id,
+    slice_output_to_gtf,
+    get_sequence,
+)
+
+logger = logging.getLogger(__name__)
+
+
+
[docs]def run_trnascan(
+    genome_file: PathLike,
+    output_dir: Path,
+    trnascan_bin: Path = Path("tRNAscan-SE"),
+    trnascan_filter: Path = Path("EukHighConfidenceFilter"),
+    num_threads: int = 1,
+) -> None:
+    """
+    Executes tRNAscan-SE on genomic slices
+        :param genome_file: Genome file path.
+        :type genome_file: PathLike 
+        :param output_dir:  working directory path.
+        :type output_dir: Path  
+        :param trnascan_bin: tRNAscan-SE software path.
+        :type trnascan_bin: Path, default tRNAscan-SE
+        :param trnascan_filter: tRNAscan-SE filter set path.
+        :type trnascan_filter: Path, default EukHighConfidenceFilter
+        :param num_threads: int, number of threads.
+        :type num_threads: int, default 1 
+                            
+        :return: None
+        :rtype: None
+    """
+    check_exe(trnascan_bin)
+    check_file(trnascan_filter)
+    trnascan_dir = create_dir(output_dir, "trnascan_output")
+    output_file = trnascan_dir / "annotation.gtf"
+    if output_file.exists():
+        transcript_count = check_gtf_content(output_file, "transcript")
+        if transcript_count > 0:
+            logger.info("Trnascan gtf file exists, skipping analysis")
+            return
+    logger.info("Creating list of genomic slices")
+    seq_region_to_length = get_seq_region_length(genome_file, 5000)
+    slice_ids_per_region = get_slice_id(seq_region_to_length, 1000000, 0, 5000)
+    trnascan_cmd = [
+        str(trnascan_bin),
+        None,
+        "-o",
+        None,
+        "-f",
+        None,
+        "-H",  # show both primary and secondary structure components to covariance model bit scores
+        "-q",  # quiet mode
+        "--detail",
+        "-Q",
+    ]
+    logger.info("Running tRNAscan-SE")
+    pool = multiprocessing.Pool(num_threads)  # pylint: disable=consider-using-with
+    for slice_id in slice_ids_per_region:
+        pool.apply_async(
+            _multiprocess_trnascan,
+            args=(
+                trnascan_cmd,
+                slice_id,
+                genome_file,
+                trnascan_filter,
+                trnascan_dir,
+            ),
+        )
+
+    pool.close()
+    pool.join()
+    slice_output_to_gtf(
+        output_dir=trnascan_dir, unique_ids=True, file_extension=".trna.gtf"
+    )
+    for gtf_file in trnascan_dir.glob("*.trna.gtf"):
+        gtf_file.unlink()

+
+
+def _multiprocess_trnascan(
+    trnascan_cmd: List[str],
+    slice_id: List[str],
+    genome_file: Path,
+    trnascan_filter: Path,
+    trnascan_dir: Path,
+) -> None:
+    """
+    Run tRNAscan-SE on multiprocess on genomic slices
+    Args:
+        trnascan_cmd: tRNAscan-SE command to execute.
+        slice_id: Slice Id to run tRNAscan-SE on.
+        genome_file : Genome file.
+        trnascan_dir : tRNAscan-SE output dir.
+        trnascan_filter: tRNAscan-SE filter set.
+    """
+    region_name, start, end = slice_id
+    logger.info(
+        "Processing slice to find tRNAs using tRNAscan-SE:%s:%s:%s",
+        region_name,
+        start,
+        end,
+    )
+    seq = get_sequence(region_name, int(start), int(end), 1, genome_file, trnascan_dir)
+    slice_name = f"{region_name}.rs{start}.re{end}"
+    slice_file = trnascan_dir / f"{slice_name}.fa"
+    with open(slice_file, "w+", encoding="utf8") as region_out:
+        region_out.write(f">{region_name}\n{seq}\n")
+    # trnscan output
+    region_results = trnascan_dir / f"{slice_name}.trna.gtf"
+    output_file = Path(f"{slice_file}.trna")
+    ss_output_file = Path(f"{output_file}.ss")
+    # filtering
+    filter_prefix_file = f"{slice_name}.filt"
+    filter_output_file = trnascan_dir / f"{filter_prefix_file}.out"
+    filter_log_file = trnascan_dir / f"{filter_prefix_file}.log"
+    filter_ss_file = trnascan_dir / f"{filter_prefix_file}.ss"
+    # trnascan_cmd = generic_trnascan_cmd.copy()
+    trnascan_cmd[1], trnascan_cmd[3], trnascan_cmd[5] = (
+        str(slice_file),
+        str(output_file),
+        str(ss_output_file),
+    )
+    logger.info("tRNAscan-SE command: %s", " ".join(trnascan_cmd))
+    subprocess.run(trnascan_cmd, check=True)
+    # If the trnascan output is empty there is no need to go on with filtering
+    if output_file.stat().st_size == 0:
+        output_file.unlink()
+        slice_file.unlink()
+        ss_output_file.unlink(missing_ok=True)
+        return
+
+    filter_cmd = [
+        str(trnascan_filter),
+        "--result",  # tRNAscan-SE output file used as input
+        str(output_file),
+        "--ss",  # tRNAscan-SE secondary structure file used as input
+        str(ss_output_file),
+        "--output",
+        str(trnascan_dir),
+        "--prefix",
+        str(filter_prefix_file),
+    ]
+    logger.info(
+        "tRNAscan-SE filter command: %s", " ".join(str(item) for item in filter_cmd)
+    )
+    subprocess.run(filter_cmd)#pylint:disable=subprocess-run-check
+    _create_trnascan_gtf(region_results, filter_output_file, region_name)
+    output_file.unlink(missing_ok=True)
+    slice_file.unlink(missing_ok=True)
+    ss_output_file.unlink(missing_ok=True)
+    Path(filter_prefix_file).unlink(missing_ok=True)
+    filter_log_file.unlink(missing_ok=True)
+    filter_ss_file.unlink(missing_ok=True)
+    filter_output_file.unlink(missing_ok=True)
+
+
+def _create_trnascan_gtf(
+    region_results: Path, filter_output_file: Path, region_name: str
+) -> None:
+    """
+    Read the fasta file and save the content in gtf format
+    All the genomic slices are collected in a single gtf output
+    Args:
+        region_results : GTF file with the results per region.
+        filter_file : GTF file with the filtered results per region.
+        region_name :Coordinates of genomic slice.
+
+    tRNAscan-SE output format:
+    col0: GtRNAdb Gene Symbol - gene ID in corresponding genome
+    col1: tRNAscan-SE ID - tRNA ID in tRNAscan-SE prediction results
+    col2-3: Locus - Genomic coordinates of predicted gene
+    col4: Isotype (from Anticodon) - tRNA isotype determined by anticodon
+    col5: Anticodon - anticodon of predicted tRNA gene
+    col6-7: Intron boundaries
+    col8: General tRNA Model Score - covariance model bit score from tRNAscan-SE results
+    col9: Best Isotype Model - best matching (highest scoring) isotype determined
+    by isotype-specific covariance model classification
+    col10-11-12: Anticodon and Isotype Model Agreement - consistency between anticodon
+    from predicted gene sequence and best isotype model
+    col13: Features - special gene features that may include gene set categorization,
+    number of introns, possible pseudogenes, possible truncation, or base-pair mismatches
+    """
+    with open(filter_output_file, "r", encoding="utf8") as trna_in, open(
+        region_results, "w+", encoding="utf8"
+    ) as trna_out:
+        gene_counter = 1
+        for line in trna_in:
+            result_match = re.search(r"^" + region_name, line)
+            if result_match:
+                results = line.split()
+                start = int(results[2])
+                end = int(results[3])
+                strand = "+"
+                if start > end:
+                    strand = "-"
+                    start, end = end, start
+                biotype = (
+                    "tRNA"
+                    if re.search(r"high confidence set", line)
+                    else "tRNA_pseudogene"
+                )
+                transcript_string = (
+                    f"{region_name}\ttRNAscan\ttranscript\t{start}\t{end}\t.\t"
+                    f'{strand}\t.\tgene_id "{gene_counter}"; transcript_id '
+                    f'"{gene_counter}"; biotype "{biotype}";\n'
+                )
+                exon_string = (
+                    f"{region_name}\ttRNAscan\texon\t{start}\t{end}\t.\t"
+                    f'{strand}\t.\tgene_id "{gene_counter}"; transcript_id '
+                    f'"{gene_counter}"; exon_number "1"; biotype "{biotype}";\n'
+                )
+                trna_out.write(transcript_string)
+                trna_out.write(exon_string)
+                trna_out.flush()
+                gene_counter += 1
+
+
+class InputSchema(argschema.ArgSchema):
+    """Input arguments expected to run tRNAscan-SE."""
+
+    genome_file = argschema.fields.InputFile(
+        required=True, description="Genome file path"
+    )
+    trnascan_bin = argschema.fields.String(
+        required=False,
+        default="tRNAscan-SE",
+        description="tRNAscan-SE executable path",
+    )
+    trnascan_filter = argschema.fields.String(
+        required=False,
+        default="/hps/software/users/ensembl/ensw/C8-MAR21-sandybridge/linuxbrew/bin/EukHighConfidenceFilter",
+        description="tRNAscan-SE filter path",
+    )
+    output_dir = argschema.fields.OutputDir(
+        required=True, description="Output directory path"
+    )
+    num_threads = argschema.fields.Integer(
+        required=False, default=1, description="Number of threads"
+    )
+
+
+def main() -> None:
+    """tRNAscan-SE's entry-point."""
+    mod = argschema.ArgSchemaParser(schema_type=InputSchema)
+    log_file_path = create_dir(mod.args["output_dir"], "log") / "trnascan.log"
+    loginipath = Path(__file__).parents[6] / "conf" / "logging.conf"
+    logging.config.fileConfig(
+        loginipath,
+        defaults={"logfilename": str(log_file_path)},
+        disable_existing_loggers=False,
+    )
+    run_trnascan(
+        mod.args["genome_file"],
+        mod.args["output_dir"],
+        mod.args["trnascan_bin"],
+        Path(mod.args["trnascan_filter"]),
+        mod.args["num_threads"],
+    )
+
+
+if __name__ == "__main__":
+    main()
+
+ +
+
+
+
+
+
+ +

Table of Contents

+

Index

+ + +
+

Search

+
+ + +
+
+ +
+
+
+
+ +
+
+
+
+ modules | + index +
+
+
+
+ +
+ + +
+
+
+
+ + + \ No newline at end of file diff --git a/_modules/ensembl/tools/anno/transcriptomic_annotation/minimap.html b/_modules/ensembl/tools/anno/transcriptomic_annotation/minimap.html new file mode 100644 index 0000000..652315c --- /dev/null +++ b/_modules/ensembl/tools/anno/transcriptomic_annotation/minimap.html @@ -0,0 +1,370 @@ + + + + + + + ensembl.tools.anno.transcriptomic_annotation.minimap — ensembl-anno 0.1 documentation + + + + + + + + + + + +
+
+
+ +
+
+
+ +

Source code for ensembl.tools.anno.transcriptomic_annotation.minimap

+# See the NOTICE file distributed with this work for additional information #pylint: disable=missing-module-docstring
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""
+Minimap2 is a pairwise sequence alignment algorithm designed for efficiently comparing nucleotide sequences.
+The algorithm uses a versatile indexing strategy to quickly find approximate matches between sequences, 
+allowing it to efficiently align long sequences against reference genomes or other sequences.
+
+Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34(18), 3094-3100.
+"""
+
+__all__ = ["run_minimap2"]
+import logging
+import logging.config
+from pathlib import Path
+import subprocess
+from typing import List
+import argschema
+
+
+from ensembl.tools.anno.utils._utils import (
+    check_exe,
+    create_dir,
+    check_gtf_content,
+)
+
+
+
[docs]def run_minimap2(
+    output_dir: Path,
+    long_read_fastq_dir: Path,
+    genome_file: Path,
+    minimap2_bin: Path = Path("minimap2"),
+    paftools_bin: Path = Path("paftools.js"),
+    max_intron_length: int = 100000,
+    num_threads: int = 1,
+) -> None:
+    """
+    Run Minimap2 to align long read data against genome file.
+    Default Minimap set for PacBio data.
+    
+        :param output_dir: Working directory path.
+        :type output_dir: Path
+        :param long_read_fastq_dir: Long read directory path.
+        :type long_read_fastq_dir: Path
+        :param genome_file: Genome file path.
+        :type genome_file: Path
+        :param minimap2_bin: Software path.
+        :type minimap2_bin: Path, default minimap2
+        :param paftools_bin: Software path.
+        :type paftools_bin: Path, default paftools.js
+        :param max_intron_length: The maximum intron size for alignments. Defaults to 100000.
+        :type max_intron_length: int, default 100000
+        :param num_threads: Number of available threads.
+        :type num_threads: int, default 1
+               
+        :return: None
+        :rtype: None
+    """
+    check_exe(minimap2_bin)
+    check_exe(paftools_bin)
+    minimap2_dir = create_dir(output_dir, "minimap2_output")
+
+    logging.info("Skip analysis if the gtf file already exists")
+    output_file = minimap2_dir / "annotation.gtf"
+    if output_file.exists():
+        transcript_count = check_gtf_content(output_file, "transcript")
+        if transcript_count > 0:
+            logging.info("Minimap2 gtf file exists, skipping analysis")
+            return
+    minimap2_index_file = minimap2_dir / f"{genome_file.name}.mmi"
+    # minimap2_hints_file = minimap2_dir /"minimap2_hints.gff"
+    file_types = ("*.fastq", "*.fq")
+    fastq_file_list = [
+        path for file_type in file_types for path in Path(long_read_fastq_dir).rglob(file_type)
+    ]
+    if len(fastq_file_list) == 0:
+        raise IndexError(f"The list of fastq files is empty. Fastq dir:\n{long_read_fastq_dir}")
+
+    if not minimap2_index_file.exists():
+        logging.info("Did not find an index file for minimap2. Will create now")
+        try:
+            subprocess.run(  # pylint:disable=subprocess-run-check
+                [
+                    minimap2_bin,
+                    "-t",
+                    str(num_threads),
+                    "-d",
+                    str(minimap2_index_file),
+                    genome_file,
+                ]
+            )
+        except subprocess.CalledProcessError as e:
+            logging.error("An error occurred while creating minimap2 index: %s", e)
+        except OSError as e:
+            logging.error("An OS error occurred: %s", e)
+
+    logging.info("Running minimap2 on the files in the long read fastq dir")
+    for fastq_file in fastq_file_list:
+        sam_file = minimap2_dir / f"{fastq_file.name}.sam"
+        bed_file = minimap2_dir / f"{fastq_file.name}.bed"
+        logging.info("Processing %s", fastq_file)
+        with open(bed_file, "w+", encoding="utf8") as bed_file_out:
+            subprocess.run(  # pylint:disable=subprocess-run-check
+                [
+                    minimap2_bin,
+                    "-G",
+                    str(max_intron_length),
+                    "-t",
+                    str(num_threads),
+                    "--cs",
+                    "--secondary=no",
+                    "-ax",
+                    "splice",
+                    "-u",
+                    "b",
+                    minimap2_index_file,
+                    fastq_file,
+                    "-o",
+                    sam_file,
+                ]
+            )
+        logging.info("Creating bed file from SAM")
+        subprocess.run(
+            [paftools_bin, "splice2bed", sam_file], stdout=bed_file_out
+        )  # pylint:disable=subprocess-run-check
+
+    bed_to_gtf(minimap2_dir)
+
+    logging.info("Completed running minimap2")

+
+
+def bed_to_gtf(output_dir: Path) -> None:
+    """
+    Convert bed file into gtf file
+    Args:
+        output_dir : Working directory path.
+    """
+    gtf_file_path = output_dir / "annotation.gtf"
+    with open(gtf_file_path, "w+", encoding="utf8") as gtf_out:
+        gene_id = 1
+        for bed_file in output_dir.glob("*.bed"):
+            logging.info("Converting bed to GTF: %s", str(bed_file))
+            with open(bed_file, "r", encoding="utf8") as bed_in:
+                for line in bed_in:
+                    elements = line.rstrip().split("\t")
+                    seq_region_name = elements[0]
+                    offset = int(elements[1])
+                    strand = elements[5]
+                    # sizes of individual block of exons
+                    block_sizes = [size for size in elements[10].split(",") if size]
+                    block_starts = [size for size in elements[11].split(",") if size]
+                    exons = bed_block_to_exons(block_sizes, block_starts, offset)
+                    transcript_start = None
+                    transcript_end = None
+                    exon_records = []
+                    for i, exon_coords in enumerate(exons):
+                        if transcript_start is None or exon_coords[0] < transcript_start:
+                            transcript_start = exon_coords[0]
+
+                        if transcript_end is None or exon_coords[1] > transcript_end:
+                            transcript_end = exon_coords[1]
+
+                        exon_line = (
+                            f"{seq_region_name}\tminimap\texon\t{exon_coords[0]}\t"
+                            f"{exon_coords[1]}\t.\t{strand}\t.\t"
+                            f'gene_id "minimap_{gene_id}"; transcript_id "minimap_{gene_id}"; '
+                            f'exon_number "{i+ 1}";\n'
+                        )
+                        exon_records.append(exon_line)
+                    transcript_line = (
+                        f"{seq_region_name}\tminimap\ttranscript\t{transcript_start}\t"
+                        f"{transcript_end}\t.\t{strand}\t.\t"
+                        f'gene_id "minimap_{gene_id}"; transcript_id "minimap_{gene_id}"\n'
+                    )
+                    gtf_out.write(transcript_line)
+                    for exon_line in exon_records:
+                        gtf_out.write(exon_line)
+                    gene_id += 1
+
+
+def bed_block_to_exons(block_sizes: List, block_starts: List, offset: int) -> List:
+    """
+    Extract exon size and start from exon feature block
+    Args:
+        block_sizes : Block feature size.
+        block_starts : Block feature starts.
+        offset : Feature offset.
+
+    Returns:
+        List of exon coordinates
+    """
+    exons = []
+    for i, _ in enumerate(block_sizes):
+        block_start = offset + int(block_starts[i]) + 1
+        block_end = block_start + int(block_sizes[i]) - 1
+        if block_end < block_start:
+            logging.warning("Warning: block end is less than block start, skipping exon")
+            continue
+        exon_coords = [str(block_start), str(block_end)]
+        exons.append(exon_coords)
+    return exons
+
+
+class InputSchema(argschema.ArgSchema):
+    """Input arguments expected to run Minimap2 software."""
+
+    output_dir = argschema.fields.OutputDir(required=True, description="Output directory path")
+    long_read_fastq_dir = argschema.fields.String(
+        required=True,
+        description="Long read directory path",
+    )
+    genome_file = argschema.fields.InputFile(required=True, description="Genome file path")
+    minimap2_bin = argschema.fields.String(
+        required=False,
+        default="minimap2",
+        description="Minimap2 software path",
+    )
+    paftools_bin = argschema.fields.String(
+        required=False,
+        default="paftools.js",
+        description="Paftools software path",
+    )
+    max_intron_length = argschema.fields.Integer(
+        required=False,
+        default="100000",
+        description="The maximum intron length.",
+    )
+    max_intron_length = argschema.fields.Integer(
+        required=False,
+        default="100000",
+        description="The maximum intron size for alignments.",
+    )
+    num_threads = argschema.fields.Integer(required=False, default=1, description="Number of threads")
+
+
+def main() -> None:
+    """Minimap2's entry-point."""
+    mod = argschema.ArgSchemaParser(schema_type=InputSchema)
+    log_file_path = create_dir(mod.args["output_dir"], "log") / "minimap.log"
+    loginipath = Path(__file__).parents[6] / "conf" / "logging.conf"
+    logging.config.fileConfig(
+        loginipath,
+        defaults={"logfilename": str(log_file_path)},
+        disable_existing_loggers=False,
+    )
+    run_minimap2(
+        mod.args["output_dir"],
+        mod.args["long_read_fastq_dir"],
+        mod.args["genome_file"],
+        mod.args["minimap2_bin"],
+        mod.args["paftools_bin"],
+        mod.args["max_intron_length"],
+        mod.args["num_threads"],
+    )
+
+ +
+
+
+
+
+
+ +

Table of Contents

+

Index

+ + +
+

Search

+
+ + +
+
+ +
+
+
+
+ +
+
+
+
+ modules | + index +
+
+
+
+ +
+ + +
+
+
+
+ + + \ No newline at end of file diff --git a/_modules/ensembl/tools/anno/transcriptomic_annotation/scallop.html b/_modules/ensembl/tools/anno/transcriptomic_annotation/scallop.html new file mode 100644 index 0000000..473e233 --- /dev/null +++ b/_modules/ensembl/tools/anno/transcriptomic_annotation/scallop.html @@ -0,0 +1,308 @@ + + + + + + + ensembl.tools.anno.transcriptomic_annotation.scallop — ensembl-anno 0.1 documentation + + + + + + + + + + + +
+
+
+ +
+
+
+ +

Source code for ensembl.tools.anno.transcriptomic_annotation.scallop

+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""
+Scallop is a high-performance tool designed for the accurate and efficient quantification 
+of transcriptome assembly. 
+It's capable of handling large-scale transcriptomic data while providing precise estimates 
+of transcript abundances.
+Scallop's algorithmic approach allows it to efficiently reconstruct transcript structures 
+and quantify their expression levels, making it a valuable resource for studying gene 
+expression and transcriptome analysis.
+
+Shao M, Kingsford C. Accurate assembly of transcripts through phase-preserving graph 
+decomposition. Nat Biotechnol.
+2017 Dec;35(12):1167-1169. doi: 10.1038/nbt.4020. Epub 2017 Nov 13. PMID: 29131147; PMCID: PMC5722698.
+"""
+
+__all__ = ["run_scallop"]
+import logging
+import logging.config
+from pathlib import Path
+import re
+import subprocess
+import argschema
+
+from ensembl.tools.anno.utils._utils import (
+    check_exe,
+    create_dir,
+    check_gtf_content,
+)
+
+
+
[docs]def run_scallop(
+    output_dir: Path,
+    scallop_bin: Path = Path("scallop"),
+    prlimit_bin: Path = Path("prlimit"),
+    stringtie_bin: Path = Path("stringtie"),
+    memory_limit: int = 40 * 1024**3,
+) -> None:
+    """
+    Run Scallop assembler on short read data after STAR alignment.
+
+        :param output_dir: Working directory path.
+        :type output_dir: Path
+        :param scallop_bin: Software path.
+        :type scallop_bin: Path, default scallop
+        :param prlimit_bin: Software path.
+        :type prlimit_bin: Path, default prlimit
+        :param stringtie_bin: Software path.
+        :type stringtie_bin: Path, default stringtie
+        :param memory_limit: Memory limit Scallop command Defaults to 40*1024**3.
+        :type memory_limit: int
+                        
+        :return: None
+        :rtype: None
+    """
+    check_exe(scallop_bin)
+    check_exe(stringtie_bin)
+    scallop_dir = create_dir(output_dir, "scallop_output")
+    logging.info("Skip analysis if the gtf file already exists")
+    output_file = scallop_dir / "annotation.gtf"
+    if output_file.exists():
+        transcript_count = check_gtf_content(output_file, "transcript")
+        if transcript_count > 0:
+            logging.info("Scallop gtf file exists, skipping analysis")
+            return
+
+    star_dir = output_dir / "star_output"
+
+    if star_dir.exists() and len(list(star_dir.glob("*.bam"))) != 0:
+        for sorted_bam_file in star_dir.glob("*.bam"):
+            transcript_file_name = re.sub(".bam", ".scallop.gtf", sorted_bam_file.name)
+            transcript_file = scallop_dir / transcript_file_name
+            if transcript_file.exists():
+                logging.info(
+                    "Found an existing stringtie gtf file, will not overwrite. \
+                        File found: %s",
+                    transcript_file,
+                )
+            else:
+                logging.info("Running Scallop on: %s", sorted_bam_file.name)
+                try:
+                    scallop_cmd = [
+                        scallop_bin,
+                        "-i",
+                        sorted_bam_file,
+                        "-o",
+                        transcript_file,
+                        "--min_flank_length",
+                        "10",
+                    ]
+                    if memory_limit is not None:
+                        scallop_cmd = prlimit_command(prlimit_bin, scallop_cmd, memory_limit)
+                    subprocess.check_output(scallop_cmd, stderr=subprocess.STDOUT, universal_newlines=True)
+                    # This combines the standard output and error streams into a single
+                    # string and ensures that the output is in text mode
+
+                except subprocess.CalledProcessError as ex:
+                    logging.error("Error occurred while running Scallop:")
+                    logging.error("Command: %s\n", " ".join(scallop_cmd))
+                    logging.error("Return code: %s\n", str(ex.returncode))
+                    logging.error("Output and error messages: %s\n", ex.output)
+    else:
+        raise IndexError(f"The list of sorted bam files is empty, Star output dir: {star_dir}")
+
+    # Now need to merge
+    logging.info("Merge Scaalop's output.")
+    scallop_merge(scallop_dir, stringtie_bin)

+
+
+def scallop_merge(scallop_dir: Path, stringtie_bin: Path = Path("stringtie")) -> None:
+    """
+    Merge Scallop result in a single gtf file
+
+    scallop_dir : Input directory's path.
+    stringtie_bin : Software path.
+    """
+    scallop_input_to_file = scallop_dir / "scallop_assemblies.txt"
+    scallop_merge_output_file = scallop_dir / "annotation.gtf"
+    with open(scallop_input_to_file, "w+", encoding="utf8") as gtf_list_out:
+        for gtf_file in scallop_dir.glob("*.scallop.gtf"):
+            transcript_count = check_gtf_content(gtf_file, "transcript")
+            if transcript_count > 0:
+                gtf_list_out.write(gtf_file + "\n")
+            else:
+                logging.warning("Warning, skipping file with no transcripts. Path:%s\n", gtf_file)
+
+    try:
+        subprocess.check_output(
+            [
+                stringtie_bin,
+                "--merge",
+                "-o",
+                scallop_merge_output_file,
+                scallop_input_to_file,
+            ],
+            stderr=subprocess.STDOUT,
+            text=True,
+        )
+
+    except subprocess.CalledProcessError as e:
+        print("StringTie execution failed with an error:%s", e.output)
+
+
+def prlimit_command(prlimit_bin, command_list, virtual_memory_limit) -> list:
+    """
+    Prepend memory limiting arguments to a command list to be run with subprocess.
+
+    This method uses the `prlimit` program to set the memory limit.
+
+    The `virtual_memory_limit` size is in bytes.
+
+    prlimit arguments:
+    -v, --as[=limits]
+           Address space limit.
+    """
+    return [str(prlimit_bin), f"-v{virtual_memory_limit}"] + command_list
+
+
+class InputSchema(argschema.ArgSchema):
+    """Input arguments expected to run StringTie software."""
+
+    output_dir = argschema.fields.OutputDir(required=True, description="Output directory path")
+    scallop_bin = argschema.fields.String(
+        required=False,
+        default="scallop",
+        description="Scallop software path",
+    )
+    prlimit_bin = argschema.fields.String(
+        required=False,
+        default="prlimit",
+        description="Prlimit software path",
+    )
+    memory_limit = argschema.fields.Integer(
+        required=False, default=40 * 1024**3, description="Memory's limit for Scallop command"
+    )
+
+
+def main() -> None:
+    """Scallop's entry-point. :no-index:"""
+    mod = argschema.ArgSchemaParser(schema_type=InputSchema)
+    log_file_path = create_dir(mod.args["output_dir"], "log") / "scallop.log"
+    loginipath = Path(__file__).parents[6] / "conf" / "logging.conf"
+    logging.config.fileConfig(
+        loginipath,
+        defaults={"logfilename": str(log_file_path)},
+        disable_existing_loggers=False,
+    )
+    run_scallop(
+        mod.args["output_dir"], mod.args["scallop_bin"], mod.args["prlimit_bin"], mod.args["memory_limit"]
+    )
+
+ +
+
+
+
+
+
+ +

Table of Contents

+

Index

+ + +
+

Search

+
+ + +
+
+ +
+
+
+
+ +
+
+
+
+ modules | + index +
+
+
+
+ +
+ + +
+
+
+
+ + + \ No newline at end of file diff --git a/_modules/ensembl/tools/anno/transcriptomic_annotation/star.html b/_modules/ensembl/tools/anno/transcriptomic_annotation/star.html new file mode 100644 index 0000000..c4d0135 --- /dev/null +++ b/_modules/ensembl/tools/anno/transcriptomic_annotation/star.html @@ -0,0 +1,727 @@ + + + + + + + ensembl.tools.anno.transcriptomic_annotation.star — ensembl-anno 0.1 documentation + + + + + + + + + + + +
+
+
+ +
+
+
+ +

Source code for ensembl.tools.anno.transcriptomic_annotation.star

+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""
+The STAR (Spliced Transcripts Alignment to a Reference) alignment tool is widely used
+in genomics research for aligning RNA-seq data to a reference genome.
+Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner.
+Bioinformatics. 2013;29(1):15-21. doi:10.1093/bioinformatics/bts635
+"""
+
+__all__ = ["run_star", "subsample_transcriptomic_data"]
+import logging
+import logging.config
+import gzip
+import math
+import multiprocessing
+from pathlib import Path
+import random
+import re
+import shutil
+import subprocess
+from typing import List
+import argschema
+
+
+from ensembl.tools.anno.utils._utils import (
+    check_exe,
+    create_dir,
+    check_gtf_content,
+    get_seq_region_length,
+)
+
+
+
[docs]def run_star(
+    genome_file: Path,
+    output_dir: Path,
+    short_read_fastq_dir: Path,
+    delete_pre_trim_fastq: bool = False,
+    trim_fastq: bool = False,
+    max_reads_per_sample: int = 0,
+    max_intron_length: int = 100000,
+    num_threads: int = 1,
+    star_bin: Path = Path("star"),
+    samtools_bin: Path = Path("samtools"),
+    trim_galore_bin: Path = Path("trim_galore"),
+) -> None:
+    """
+    Run STAR alignment on list of short read data.
+        :param genome_file: Genome file path.
+        :type genome_file: Path
+        :param output_dir: Working directory path.
+        :type output_dir: Path
+        :param short_read_fastq_dir: Short read directory path.
+        :type short_read_fastq_dir: Path
+        :param delete_pre_trim_fastq: Delete the original fastq files after trimming. Defaults to False.
+        :type delete_pre_trim_fastq: boolean, default False
+        :param trim_fastq: Trim short read files using TrimGalore. Defaults to False.
+        :type trim_fastq: boolean, default False
+        :param max_reads_per_sample: Max number of reads per sample. Defaults to 0 (unlimited).
+        :type max_reads_per_sample: int, default 0
+        :param max_intron_length: The maximum intron size for alignments. Defaults to 100000.
+        :type max_intron_length: int, default 100000
+        :param num_threads: Number of available threads.
+        :type num_threads: int, default 1 
+        :param star_bin: Software path.
+        :type star_bin: Path, default star
+        :param samtools_bin: Software path.
+        :type samtools_bin: Path,default samtools
+        :param trim_galore_bin: Software path.
+        :type trim_galore_bin: Path, default trim_galore
+                        
+        :return: None
+        :rtype: None
+    """
+    check_exe(star_bin)
+    # If trimming has been enabled then switch the path for
+    # short_read_fastq_dir from the original location to the trimmed fastq dir
+    if trim_fastq:
+        run_trimming(output_dir, short_read_fastq_dir, delete_pre_trim_fastq, num_threads, trim_galore_bin)
+        short_read_fastq_dir = output_dir / "trim_galore_output"
+
+    #  if not os.path.exists(subsample_script_path):
+    #subsample_script_path = "subsample_fastq.py"
+
+    star_dir = create_dir(output_dir, "star_output")
+
+    for output_file in [
+        output_dir / "stringtie_output/annotation.gtf",
+        output_dir / "scallop_output/annotation.gtf",
+    ]:
+        if output_file.exists():
+            transcript_count = check_gtf_content(output_file, "transcript")  # check a gtf
+            if transcript_count > 0:
+                logging.info("Transcriptomic alignment exists")
+                return
+
+    star_index_file = star_dir / "SAindex"
+    fastq_file_list = []
+    file_types = ("*.fastq", "*.fq", "*.fastq.gz", "*.fq.gz")
+    fastq_file_list = [
+        path for file_type in file_types for path in Path(short_read_fastq_dir).rglob(file_type)
+    ]
+    if len(fastq_file_list) == 0:
+        raise IndexError(f"The list of fastq files is empty. Fastq dir:\n{short_read_fastq_dir}")
+
+
+    # for file_type in file_types:
+    #    fastq_file_list.extend(glob.glob(os.path.join(short_read_fastq_dir, file_type)))
+
+    # Get list of paired paths
+    fastq_file_list = _create_paired_paths(fastq_file_list)
+    # Subsamples in parallel if there's a value set
+    if max_reads_per_sample:
+        subsample_transcriptomic_data(fastq_file_list)
+        # Get the list of the new subsampled files
+        fastq_file_list = [
+            path for file_type in file_types for path in Path(short_read_fastq_dir).rglob(file_type)
+        ]
+    # I don't think is needed
+    # fastq_file_list = check_for_fastq_subsamples(fastq_file_list)
+
+    if not star_index_file.exists():
+        logging.info("Did not find an index file for Star. Will create now")
+        seq_region_to_length = get_seq_region_length(genome_file, 0)
+        genome_size = sum(seq_region_to_length.values())
+        # This calculates the base-2 logarithm of the genome_size. The logarithm of the genome size is
+        # a measure of how many bits are needed to represent the genome size in binary.
+        #
+        # The choice of 14 as the maximum value is likely based on empirical observations and optimization
+        # considerations. Too large of a seed length can lead to increased memory usage and potentially
+        # slower indexing, while a seed length that is too small might affect alignment accuracy.
+        index_bases = min(14, math.floor((math.log(genome_size, 2) / 2) - 1))
+        try:
+            subprocess.run(#pylint:disable=subprocess-run-check
+            [
+                str(star_bin),
+                "--runThreadN",
+                str(num_threads),
+                "--runMode",
+                "genomeGenerate",
+                "--outFileNamePrefix",
+                f"{star_dir}/",
+                "--genomeDir",
+                str(star_dir),
+                "--genomeSAindexNbases",
+                str(index_bases),
+                "--genomeFastaFiles",
+                str(genome_file),
+            ]
+            )
+        except  Exception as e:
+            logging.error("An error occurred while creating star index: %s", e)
+      
+    logging.info("Running Star on the files in the fastq dir")
+    for fastq_file in fastq_file_list:
+        # logger.info(fastq_file_path)
+        # fastq_file_name = os.path.basename(fastq_file_path)
+        star_tmp_dir = star_dir / "tmp"
+        if star_tmp_dir.exists():
+            shutil.rmtree(star_tmp_dir)
+        sam_file = Path(f"{star_dir}/{fastq_file.name}.sam")
+        junctions_file = Path(f"{star_dir}/{fastq_file.name}.sj.tab")
+        sam_file_name = sam_file.name
+        sam_temp_file = Path(f"{star_dir}/{sam_file_name}.tmp")
+        bam_file = re.sub(".sam", ".bam", sam_file_name)
+        bam_sort_file = Path(f"{star_dir}/{bam_file}")
+        log_out_file = Path(f"{star_dir}/{fastq_file.name}.Log.final.out")
+        if log_out_file.exists() and bam_sort_file.exists() and bam_sort_file.stat().st_size != 0:
+            logging.info(
+                "Found an existing bam file for the fastq file, \
+                presuming the file has been processed, will skip"
+            )
+            continue
+
+        logging.info("Processing %s", fastq_file)
+        star_command = [
+            str(star_bin),
+            "--outFilterIntronMotifs",
+            "RemoveNoncanonicalUnannotated",
+            "--outSAMstrandField",
+            "intronMotif",
+            "--runThreadN",
+            str(num_threads),
+            "--twopassMode",
+            "Basic",
+            "--runMode",
+            "alignReads",
+            "--genomeDir",
+            str(star_dir),
+            "--readFilesIn",
+            str(fastq_file),
+            "--outFileNamePrefix",
+            f"{star_dir}/",
+            "--outTmpDir",
+            str(star_tmp_dir),
+            "--outSAMtype",
+            "SAM",
+            "--alignIntronMax",
+            str(max_intron_length),
+        ]
+        #'--outSJfilterIntronMaxVsReadN','5000','10000','25000','40000',
+        #'50000','50000','50000','50000','50000','100000']
+        check_compression = re.search(r".gz$", fastq_file)
+        if check_compression:
+            star_command.append("--readFilesCommand")
+            star_command.append("gunzip")
+            star_command.append("-c")
+        subprocess.run(star_command)#pylint:disable=subprocess-run-check
+        shutil.move(Path(f"{star_dir}/Aligned.out.sam"), sam_file)
+        shutil.move(Path(f"{star_dir}/SJ.out.tab"), junctions_file)
+        logging.info("Converting samfile into sorted bam file. Bam file: %s", bam_file)
+        subprocess.run(#pylint:disable=subprocess-run-check
+            [
+                str(samtools_bin),
+                "sort",
+                "-@",
+                str(num_threads),
+                "-T",
+                str(sam_temp_file),
+                "-o",
+                str(bam_sort_file),
+                str(sam_file),
+            ]
+        )
+        shutil.move(star_dir / "Log.final.out", log_out_file)
+        sam_file.unlink()
+    logging.info("Completed running STAR")

+
+
+def _create_paired_paths(fastq_file_paths: List) -> List:
+    """
+    Create list of paired transcriptomic fastq files
+
+    Args:
+        fastq_file_paths (List): List of transcriptomic file paths.
+
+    Returns:
+        List: List of paired transcriptomic files
+    """
+    path_dict = {}
+    # final_list = []
+    for fastq_file in fastq_file_paths:
+        paired_name = re.search(r"(.+)_\d+\.(fastq|fq)", fastq_file)
+        if not paired_name:
+            logging.exception(
+                "Could not find _1 or _2 at the end of the prefix \
+                for file. Assuming file is not paired: %s",
+                fastq_file,
+            )
+            # final_list.append([fastq_file])
+            path_dict[fastq_file] = [fastq_file]
+            continue
+        run_accession = paired_name.group(1)
+        if run_accession in path_dict:
+            path_dict[run_accession].append(fastq_file)
+        else:
+            path_dict[run_accession] = [fastq_file]
+    # for pair in path_dict:
+    #    final_list.append(path_dict[pair])
+    logging.info([value for values_list in path_dict.values() for value in values_list])
+    return [value for values_list in path_dict.values() for value in values_list]
+
+#pylint:disable=pointless-string-statement
+"""
+For an advanced and optimised subsampling we could use 
+https://github.com/lh3/seqtk 
+"""
+
+
+def _subsample_paired_fastq_files(
+    fastq_files: List[Path],
+    output_files: List[Path] = "",
+    subsample_read_limit: int = 100000000,
+    num_threads: int = 2,
+    compressed: bool = False,
+) -> None:
+    """
+    Perform subsampling on two paired FastQ files in parallel using multiple threads.
+
+    Args:
+        fastq_files : Path for paired fastq files.
+        output_files : Path for the output file.
+        subsample_read_limit : Subsample size, defaults to 100000000.
+        num_threads : Number of threads, defaults to 2.
+        compressed : file compressed, defaults to False.
+    """
+    fastq_file_1, fastq_file_2 = fastq_files
+    if len(output_files) == 0:
+        output_files = [f"{fastq_file_1}.sub", f"{fastq_file_2}.sub"]
+    output_file_1, output_file_2 = output_files
+    if re.search(r"\.gz$", fastq_file_1):
+        compressed = True
+        num_lines = sum(1 for line in gzip.open(fastq_file_1))#pylint:disable=consider-using-with
+    else:
+        num_lines = sum(1 for line in open(fastq_file_1))#pylint:disable=consider-using-with
+
+    range_limit = int(num_lines / 4)
+    if range_limit <= subsample_read_limit:
+        logging.info("Number of reads (%s is less than the max allowed read count (%s), \
+            no need to subsample", str(range_limit),str(subsample_read_limit)
+        )
+        return
+
+    rand_list = random.sample(range(0, range_limit - 1), subsample_read_limit)
+    random_indices = {idx * 4: 1 for idx in rand_list}
+    logging.info("Processing paired files in parallel")
+    pool = multiprocessing.Pool(int(num_threads))#pylint:disable=consider-using-with
+    pool.apply_async(
+        _subsample_fastq_subset,
+        args=(
+            fastq_file_1,
+            output_file_1,
+            random_indices,
+            compressed,
+        ),
+    )
+    pool.apply_async(
+        _subsample_fastq_subset,
+        args=(
+            fastq_file_2,
+            output_file_2,
+            random_indices,
+            compressed,
+        ),
+    )
+    pool.close()
+    pool.join()
+
+
+def _subsample_fastq_subset(
+    fastq_file: Path, output_file: Path, random_indices: dict, compressed: bool
+) -> None:
+    """
+    Selecting specific sets of four lines from an input FastQ file and writing them to an output file.
+
+    Args:
+        fastq_file : Path for the fastq file.
+        output_file : Path for the output file.
+        random_indices : set of random indices.
+        compressed : the files is compressed
+    """
+    line_index = 0
+
+    with gzip.open(fastq_file, "rt") if compressed else open(fastq_file) as file_in, open(
+        output_file, "w+"
+    ) as file_out:
+        lines = [file_in.readline() for _ in range(4)]
+        while lines[3]:  # This ensures that the loop continues until the end of the input file.
+            if line_index in random_indices:
+                file_out.writelines(lines)
+            line_index += 4
+            lines = [file_in.readline() for _ in range(4)]
+
+
+
[docs]def subsample_transcriptomic_data(fastq_file_list: List[Path], num_threads: int = 2) -> None:
+    """
+    Subsample paired fastq files.
+
+    Args:
+        fastq_file_list : List of fastq file path to process.
+        num_threads : number of threads
+    """
+    for fastq_files in fastq_file_list:
+        fastq_file_1, fastq_file_2 = fastq_files
+        # fastq_file_pair = ""
+        # if len(fastq_files) == 2:
+        #    fastq_file_pair = fastq_files[1]
+
+        if len(fastq_files) == 1:
+            fastq_file_1 = fastq_files[0]
+            if Path(f"{fastq_file_1}.sub").exists():
+                logging.info(
+                    "Found an existing .sub file on the fastq path, will use that instead. File:%s.sub",
+                    fastq_file_1,
+                )
+            else:
+                _subsample_paired_fastq_files(fastq_files, compressed=True, num_threads=num_threads)
+
+        elif len(fastq_files) == 2:
+            fastq_file_1, fastq_file_2 = fastq_files
+            if Path(f"{fastq_file_1}.sub").exists() and Path(f"{fastq_file_2}.sub").exists():
+                logging.info(
+                    "Found an existing .sub files on the fastq path for both members of the pair, will use \
+                    those instead of subsampling again. Files: %s.sub,%s.sub",
+                    fastq_file_1,
+                    fastq_file_2,
+                )
+            elif Path(f"{fastq_file_2}.sub").exists():
+                _subsample_paired_fastq_files(fastq_files, compressed=True, num_threads=num_threads)

+
+
+def run_trimming(
+    output_dir: Path,
+    short_read_fastq_dir: Path,
+    delete_pre_trim_fastq: bool = False,
+    num_threads: int = 1,
+    trim_galore_bin="trim_galore",
+) -> None:
+    """
+    Trim list of short read fastq files.
+    Args:
+        output_dir : Working directory path.
+        short_read_fastq_dir : Short read directory path.
+        delete_pre_trim_fastq : Removing original fastq file post trimming. Defaults to False.
+        num_threads : Number of threads.
+        trim_galore_bin : Software path.
+    """
+    check_exe(trim_galore_bin)
+    trim_dir = create_dir(output_dir, "trim_galore_output")
+
+    fastq_file_list = []
+    file_types = ("*.fastq", "*.fq", "*.fastq.gz", "*.fq.gz")
+    fastq_file_list = [
+        path for file_type in file_types for path in Path(short_read_fastq_dir).rglob(file_type)
+    ]
+    fastq_file_list = _create_paired_paths(fastq_file_list)
+
+    trim_galore_cmd = [
+        str(trim_galore_bin),
+        "--illumina",
+        "--quality",
+        "20",
+        "--length",
+        "50",
+        "--output_dir",
+        str(trim_dir),
+    ]
+
+    pool = multiprocessing.Pool(int(num_threads))  # pylint:disable=consider-using-with
+    for fastq_paired_files in fastq_file_list:
+        pool.apply_async(
+            multiprocess_trim_galore,
+            args=(
+                trim_galore_cmd,
+                fastq_paired_files,
+                trim_dir,
+            ),
+        )
+        if delete_pre_trim_fastq:
+            for file_path in fastq_paired_files:
+                file_path.unlink()
+    pool.close()
+    pool.join()
+
+    trimmed_fastq_list = trim_dir.glob("*.fq.gz")
+
+    for trimmed_fastq_path in trimmed_fastq_list:
+        logging.info("Trimmed file path: %s", str(trimmed_fastq_path))
+        sub_patterns = re.compile(r"|".join(("_val_1.fq", "_val_2.fq", "_trimmed.fq")))
+        updated_file_path = sub_patterns.sub(".fq", trimmed_fastq_path.name)
+        updated_file_path = short_read_fastq_dir / updated_file_path
+        logging.info("Updated file path: %s", str(updated_file_path))
+        trimmed_fastq_path.rename(updated_file_path)
+
+    files_to_delete_list = []
+    for file_type in file_types:
+        files_to_delete_list.extend(short_read_fastq_dir.glob(file_type))
+
+    for file_to_delete in files_to_delete_list:
+        file_to_delete.unlink()
+
+
+def multiprocess_trim_galore(trim_galore_cmd: List, fastq_paired_files: List[Path]) -> None:
+    """
+    Trim short paired or single short read fastq file.
+    Args:
+        trim_galore_cmd : Generic command.
+        fastq_paired_files : List of single or paired fastq files.
+    """
+
+    fastq_file = fastq_paired_files[0]
+    fastq_file_pair = None
+
+    if len(fastq_paired_files) == 2:
+        fastq_file, fastq_file_pair = fastq_paired_files
+        trim_galore_cmd.append("--paired")
+        trim_galore_cmd.append(fastq_file)
+        trim_galore_cmd.append(fastq_file_pair)
+    elif len(fastq_paired_files) == 1:
+        trim_galore_cmd.append(fastq_paired_files)
+
+    logging.info("Running Trim Galore with the following command: %s", {" ".join(trim_galore_cmd)})
+    subprocess.run(trim_galore_cmd, check=True)
+
+
+class InputSchema(argschema.ArgSchema):
+    """Input arguments expected to run STAR software."""
+
+    genome_file = argschema.fields.InputFile(required=True, description="Genome file path")
+    output_dir = argschema.fields.OutputDir(required=True, description="Output directory path")
+    short_read_fastq_dir = argschema.fields.String(
+        required=True,
+        description="Short read directory path",
+    )
+    delete_pre_trim_fastq = argschema.fields.Bool(
+        required=False,
+        default=False,
+        description="Delete the original fastq files after trimming",
+    )
+    trim_fastq = argschema.fields.Bool(
+        required=False,
+        default=False,
+        description="Trim the short read files using Trim Galore",
+    )
+    max_reads_per_sample = argschema.fields.Integer(
+        required=False,
+        default="0",
+        description="The maximum number of reads to use per sample.",
+    )
+    max_intron_length = argschema.fields.Integer(
+        required=False,
+        default="100000",
+        description="The maximum intron size for alignments.",
+    )
+    num_threads = argschema.fields.Integer(required=False, default=1, description="Number of threads")
+    star_bin = argschema.fields.String(
+        required=False,
+        default="star",
+        description="Star software path",
+    )
+    samtools_bin = argschema.fields.String(
+        required=False,
+        default="samtools",
+        description="Samtools software path",
+    )
+    trim_galore_bin = argschema.fields.String(
+        required=False,
+        default="trim_galore",
+        description="Trim Galore software path",
+    )
+
+
+def main() -> None:
+    """STAR's entry-point."""
+    mod = argschema.ArgSchemaParser(schema_type=InputSchema)
+    log_file_path = create_dir(mod.args["output_dir"], "log") / "star.log"
+    loginipath = Path(__file__).parents[6] / "conf" / "logging.conf"
+    logging.config.fileConfig(
+        loginipath,
+        defaults={"logfilename": str(log_file_path)},
+        disable_existing_loggers=False,
+    )
+    run_star(
+        mod.args["genome_file"],
+        mod.args["output_dir"],
+        mod.args["short_read_fastq_dir"],
+        mod.args["delete_pre_trim_fastq"],
+        mod.args["trim_fastq"],
+        mod.args["max_reads_per_sample"],
+        mod.args["max_intron_length"],
+        mod.args["num_threads"],
+        mod.args["star_bin"],
+        mod.args["samtools_bin"],
+        mod.args["trim_galore_bin"],
+    )
+
+
+# pylint:disable=pointless-string-statement
+"""
+def model_builder(work_dir):
+
+    star_output_dir = os.path.join(work_dir, "star_output")
+
+    all_junctions_file = os.path.join(star_output_dir, "all_junctions.sj")
+    sjf_out = open(all_junctions_file, "w+")
+
+    for sj_tab_file in glob.glob(input_dir + "/*.sj.tab"):
+        sjf_in = open(sj_tab_file)
+        sjf_lines = sjf_in.readlines()
+        for line in sjf_lines:
+            elements = line.split("\t")
+            strand = "+"
+
+            #    my $slice_name = $eles[0];
+            #    my $start = $eles[1];
+            #    my $end = $eles[2];
+            #    my $strand = $eles[3];
+
+            # If the strand is undefined then skip, Augustus expects a strand
+            if elements[3] == "0":
+                continue
+            elif elements[3] == "2":
+                strand = "-"
+
+            junction_length = int(elements[2]) - int(elements[1]) + 1
+            if junction_length < 100:
+                continue
+
+            if not elements[4] and elements[7] < 10:
+                continue
+
+            # For the moment treat multimapping and single
+            # mapping things as a combined score
+            score = float(elements[6]) + float(elements[7])
+            score = str(score)
+            output_line = [
+                elements[0],
+                "RNASEQ",
+                "intron",
+                elements[1],
+                elements[2],
+                score,
+                strand,
+                ".",
+                ("src=W;mul=" + score + ";"),
+            ]
+            sjf_out.write("\t".join(output_line) + "\n")
+
+    sjf_out.close()
+"""
+
+ +
+
+
+
+
+
+ +

Table of Contents

+

Index

+ + +
+

Search

+
+ + +
+
+ +
+
+
+
+ +
+
+
+
+ modules | + index +
+
+
+
+ +
+ + +
+
+
+
+ + + \ No newline at end of file diff --git a/_modules/ensembl/tools/anno/transcriptomic_annotation/stringtie.html b/_modules/ensembl/tools/anno/transcriptomic_annotation/stringtie.html new file mode 100644 index 0000000..9609284 --- /dev/null +++ b/_modules/ensembl/tools/anno/transcriptomic_annotation/stringtie.html @@ -0,0 +1,257 @@ + + + + + + + ensembl.tools.anno.transcriptomic_annotation.stringtie — ensembl-anno 0.1 documentation + + + + + + + + + + + +
+
+
+ +
+
+
+ +

Source code for ensembl.tools.anno.transcriptomic_annotation.stringtie

+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""
+StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
+It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and
+quantitate full-length transcripts representing multiple splice variants for each gene locus.
+Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT & Salzberg SL. StringTie enables improved 
+reconstruction of a transcriptome from RNA-seq reads Nature Biotechnology 2015, doi:10.1038/nbt.3122
+"""
+
+__all__ = ["run_stringtie"]
+import logging
+import logging.config
+from pathlib import Path
+import re
+import subprocess
+import argschema
+
+from ensembl.tools.anno.utils._utils import (
+    check_exe,
+    create_dir,
+    check_gtf_content,
+)
+
+
+
[docs]def run_stringtie(
+    output_dir: Path,
+    stringtie_bin: Path = Path("stringtie"),
+    num_threads: int = 1,
+) -> None:
+    """
+    StringTie assembler of short read data.
+        :param output_dir: Working directory path.
+        :type output_dir: Path
+        :param stringtie_bin: Software path.
+        :type stringtie_bin: Path, default stringtie
+        :param num_threads: Number of available threads.
+        :type num_threads: int, default 1
+                        
+        :return: None
+        :rtype: None
+    """
+    check_exe(stringtie_bin)
+    stringtie_dir = create_dir(output_dir, "stringtie_output")
+    logging.info("Skip analysis if the gtf file already exists")
+    output_file = stringtie_dir / "annotation.gtf"
+    if output_file.exists():
+        transcript_count = check_gtf_content(output_file, "transcript")
+        if transcript_count > 0:
+            logging.info("Stringtie gtf file exists, skipping analysis")
+            return
+
+    stringtie_merge_input_file = stringtie_dir / "stringtie_assemblies.txt"
+    stringtie_merge_output_file = stringtie_dir / "annotation.gtf"
+    star_dir = output_dir / "star_output"
+
+    if star_dir.exists() and len(list(star_dir.glob("*.bam"))) != 0:
+        for sorted_bam_file in star_dir.glob("*.bam"):
+            transcript_file_name = re.sub(".bam", ".stringtie.gtf", sorted_bam_file.name)
+            transcript_file = stringtie_dir / transcript_file_name
+            if transcript_file.exists():
+                logging.info(
+                    "Found an existing stringtie gtf file, will not overwrite. \
+                        File found: %s",
+                    transcript_file,
+                )
+            else:
+                logging.info("Running Stringtie on: %s", sorted_bam_file.name)
+                try:
+                    subprocess.check_output(  # pylint:disable=subprocess-run-check
+                        [
+                            stringtie_bin,
+                            sorted_bam_file,
+                            "-o",
+                            transcript_file,
+                            "-p",
+                            str(num_threads),
+                            "-t",  # disable trimming of predicted transcripts based on coverage
+                            "-a",  # minimum anchor length for junctions
+                            "15",
+                        ]
+                    )
+                except subprocess.CalledProcessError as e:
+                    logging.error("Error running Stringtie command: %s", e)
+                    logging.error("Return code: %s", str(e.returncode))
+                    logging.error("Output and error messages:%s\n", e.output)
+    else:
+        raise IndexError(f"The list of sorted bam files is empty, Star output dir: {star_dir}")
+
+    logging.info("Creating Stringtie merge input file: %s", stringtie_merge_input_file)
+    with open(stringtie_merge_input_file, "w+", encoding="utf8") as gtf_list_out:
+        for gtf_file in stringtie_dir.glob("*.stringtie.gtf"):
+            transcript_count = check_gtf_content(gtf_file, "transcript")
+            if transcript_count > 0:
+                gtf_list_out.write(f"{gtf_file}\n")
+            else:
+                logging.warning("Warning, skipping file with no transcripts. Path:%s", gtf_file)
+    logging.info("Merging Stringtie results.")
+    try:
+        subprocess.run(  # pylint:disable=subprocess-run-check
+            [
+                stringtie_bin,
+                "--merge",
+                "-o",
+                stringtie_merge_output_file,
+                stringtie_merge_input_file,
+            ]
+        )
+    except subprocess.CalledProcessError as e:
+        logging.error("Error running Stringtie merging command: %s", e)

+
+
+class InputSchema(argschema.ArgSchema):
+    """Input arguments expected to run StringTie software."""
+
+    output_dir = argschema.fields.OutputDir(required=True, description="Output directory path")
+    stringtie_bin = argschema.fields.String(
+        required=False,
+        default="stringtie",
+        description="StringTie software path",
+    )
+    num_threads = argschema.fields.Integer(required=False, default=1, description="Number of threads")
+
+
+def main() -> None:
+    """StringTie's entry-point."""
+    mod = argschema.ArgSchemaParser(schema_type=InputSchema)
+    log_file_path = create_dir(mod.args["output_dir"], "log") / "stringtie.log"
+    loginipath = Path(__file__).parents[6] / "conf" / "logging.conf"
+    logging.config.fileConfig(
+        loginipath,
+        defaults={"logfilename": str(log_file_path)},
+        disable_existing_loggers=False,
+    )
+    run_stringtie(
+        mod.args["output_dir"],
+        mod.args["stringtie_bin"],
+        mod.args["num_threads"],
+    )
+
+ +
+
+
+
+
+
+ +

Table of Contents

+

Index

+ + +
+

Search

+
+ + +
+
+ +
+
+
+
+ +
+
+
+
+ modules | + index +
+
+
+
+ +
+ + +
+
+
+
+ + + \ No newline at end of file diff --git a/_modules/index.html b/_modules/index.html new file mode 100644 index 0000000..8777d03 --- /dev/null +++ b/_modules/index.html @@ -0,0 +1,117 @@ + + + + + + + Overview: module code — ensembl-anno 0.1 documentation + + + + + + + + + + + +
+
+
+ +
+
+
+ +

All modules for which code is available

+ + +
+
+
+
+
+
+ +

Table of Contents

+

Index

+ + +
+

Search

+
+ + +
+
+ +
+
+
+
+ +
+
+
+
+ modules | + index +
+
+
+
+ +
+ + +
+
+
+
+ + + \ No newline at end of file diff --git a/_sources/cpg.rst.txt b/_sources/cpg.rst.txt new file mode 100644 index 0000000..8603218 --- /dev/null +++ b/_sources/cpg.rst.txt @@ -0,0 +1,8 @@ +CpG Module Documentation +============================== + +.. automodule:: ensembl.tools.anno.simple_feature_annotation.cpg + :members: + :undoc-members: + :show-inheritance: + diff --git a/_sources/dust.rst.txt b/_sources/dust.rst.txt new file mode 100644 index 0000000..f1a98b4 --- /dev/null +++ b/_sources/dust.rst.txt @@ -0,0 +1,8 @@ +DustMasker Module Documentation +=================================== + +.. automodule:: ensembl.tools.anno.repeat_annotation.dust + :members: + :undoc-members: + :show-inheritance: + diff --git a/_sources/eponine.rst.txt b/_sources/eponine.rst.txt new file mode 100644 index 0000000..e460382 --- /dev/null +++ b/_sources/eponine.rst.txt @@ -0,0 +1,8 @@ +Eponine Module Documentation +============================== + +.. automodule:: ensembl.tools.anno.simple_feature_annotation.eponine + :members: + :undoc-members: + :show-inheritance: + diff --git a/_sources/genblast.rst.txt b/_sources/genblast.rst.txt new file mode 100644 index 0000000..401f411 --- /dev/null +++ b/_sources/genblast.rst.txt @@ -0,0 +1,8 @@ +Genblast Module Documentation +============================== + +.. automodule:: ensembl.tools.anno.protein_annotation.genblast + :members: + :undoc-members: + :show-inheritance: + diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt new file mode 100644 index 0000000..add9008 --- /dev/null +++ b/_sources/index.rst.txt @@ -0,0 +1,58 @@ +.. See the NOTICE file distributed with this work for additional information + regarding copyright ownership. + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. + +.. ensembl-anno documentation master file, created by + sphinx-quickstart on Fri Sep 1 12:25:36 2023. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +======================================== +Ensembl-anno +======================================== + +Anno tool kit + + +Contents +-------- +Check out :ref:`installation ` section for further information on how +to install the project. + +.. toctree:: + :maxdepth: 1 + :caption: Index + + install + license + + cpg + dust + eponine + genblast + minimap + red + repeatmasker + scallop + star + stringtie + trf + trnascan + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` \ No newline at end of file diff --git a/_sources/install.rst.txt b/_sources/install.rst.txt new file mode 100644 index 0000000..997e6c0 --- /dev/null +++ b/_sources/install.rst.txt @@ -0,0 +1,54 @@ +.. See the NOTICE file distributed with this work for additional information + regarding copyright ownership. + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. + +API Setup and installation +=========================== + +Requirements +-------------- + +.. _install: + +An Ensembl API checkout including: + +- ensembl-production `ensembl-production `_. +- ensembl-analysis `ensembl-analysis `_. (on dev/hive_master branch) +- ensembl-taxonomy `ensembl-taxonomy `_. +- ensembl-orm `ensembl-orm `_. + +Software +^^^^^^^^ + +#. Python 3.8+ +#. Bioperl 1.6.9+ + +Python Modules +^^^^^^^^^^^^^^ +#. argschema + + + +Installation +------------ +Directly from GitHub: + +.. code-block:: none + :linenos: + + git clone https://github.com/Ensembl/ensembl-analysis -b experimental/gbiab + git clone https://github.com/Ensembl/ensembl-production + git clone https://github.com/Ensembl/ensembl-hive + git clone https://github.com/Ensembl/ensembl-taxonomy + git clone https://github.com/Ensembl/ensembl-orm \ No newline at end of file diff --git a/_sources/license.rst.txt b/_sources/license.rst.txt new file mode 100644 index 0000000..9e9b2fe --- /dev/null +++ b/_sources/license.rst.txt @@ -0,0 +1,203 @@ +License +------- + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + + 1. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. \ No newline at end of file diff --git a/_sources/minimap.rst.txt b/_sources/minimap.rst.txt new file mode 100644 index 0000000..bf3a45c --- /dev/null +++ b/_sources/minimap.rst.txt @@ -0,0 +1,8 @@ +Minimap2 Module Documentation +============================== + +.. automodule:: ensembl.tools.anno.transcriptomic_annotation.minimap + :members: + :undoc-members: + :show-inheritance: + diff --git a/_sources/red.rst.txt b/_sources/red.rst.txt new file mode 100644 index 0000000..26743cd --- /dev/null +++ b/_sources/red.rst.txt @@ -0,0 +1,8 @@ +Red Module Documentation +============================== + +.. automodule:: ensembl.tools.anno.repeat_annotation.red + :members: + :undoc-members: + :show-inheritance: + diff --git a/_sources/repeatmasker.rst.txt b/_sources/repeatmasker.rst.txt new file mode 100644 index 0000000..dd07f72 --- /dev/null +++ b/_sources/repeatmasker.rst.txt @@ -0,0 +1,8 @@ +Repeatmasker Module Documentation +==================================== + +.. automodule:: ensembl.tools.anno.repeat_annotation.repeatmasker + :members: + :undoc-members: + :show-inheritance: + diff --git a/_sources/scallop.rst.txt b/_sources/scallop.rst.txt new file mode 100644 index 0000000..744055b --- /dev/null +++ b/_sources/scallop.rst.txt @@ -0,0 +1,8 @@ +Scallop Module Documentation +============================== + +.. automodule:: ensembl.tools.anno.transcriptomic_annotation.scallop + :members: + :undoc-members: + :show-inheritance: + diff --git a/_sources/star.rst.txt b/_sources/star.rst.txt new file mode 100644 index 0000000..d83c66b --- /dev/null +++ b/_sources/star.rst.txt @@ -0,0 +1,8 @@ +STAR Module Documentation +============================== + +.. automodule:: ensembl.tools.anno.transcriptomic_annotation.star + :members: + :undoc-members: + :show-inheritance: + diff --git a/_sources/stringtie.rst.txt b/_sources/stringtie.rst.txt new file mode 100644 index 0000000..980dcbd --- /dev/null +++ b/_sources/stringtie.rst.txt @@ -0,0 +1,8 @@ +Stringtie Module Documentation +================================== + +.. automodule:: ensembl.tools.anno.transcriptomic_annotation.stringtie + :members: + :undoc-members: + :show-inheritance: + diff --git a/_sources/trf.rst.txt b/_sources/trf.rst.txt new file mode 100644 index 0000000..9268f3c --- /dev/null +++ b/_sources/trf.rst.txt @@ -0,0 +1,8 @@ +TRF Module Documentation +============================== + +.. automodule:: ensembl.tools.anno.repeat_annotation.trf + :members: + :undoc-members: + :show-inheritance: + diff --git a/_sources/trnascan.rst.txt b/_sources/trnascan.rst.txt new file mode 100644 index 0000000..6193545 --- /dev/null +++ b/_sources/trnascan.rst.txt @@ -0,0 +1,8 @@ +tRNAscan-SE Module Documentation +=================================== + +.. automodule:: ensembl.tools.anno.snc_rna_annotation.trnascan + :members: + :undoc-members: + :show-inheritance: + diff --git a/_static/agogo.css b/_static/agogo.css new file mode 100644 index 0000000..401127b --- /dev/null +++ b/_static/agogo.css @@ -0,0 +1,549 @@ +/* + * agogo.css_t + * ~~~~~~~~~~~ + * + * Sphinx stylesheet -- agogo theme. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +* { + margin: 0px; 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+ margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; 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+ +const _ready = (callback) => { + if (document.readyState !== "loading") { + callback(); + } else { + document.addEventListener("DOMContentLoaded", callback); + } +}; + +/** + * Small JavaScript module for the documentation. + */ +const Documentation = { + init: () => { + Documentation.initDomainIndexTable(); + Documentation.initOnKeyListeners(); + }, + + /** + * i18n support + */ + TRANSLATIONS: {}, + PLURAL_EXPR: (n) => (n === 1 ? 0 : 1), + LOCALE: "unknown", + + // gettext and ngettext don't access this so that the functions + // can safely bound to a different name (_ = Documentation.gettext) + gettext: (string) => { + const translated = Documentation.TRANSLATIONS[string]; + switch (typeof translated) { + case "undefined": + return string; // no translation + case "string": + return translated; // translation exists + default: + return translated[0]; // (singular, plural) translation tuple exists + } + }, + + ngettext: (singular, plural, n) => { + const translated = Documentation.TRANSLATIONS[singular]; + if (typeof translated !== "undefined") + return translated[Documentation.PLURAL_EXPR(n)]; + return n === 1 ? singular : plural; + }, + + addTranslations: (catalog) => { + Object.assign(Documentation.TRANSLATIONS, catalog.messages); + Documentation.PLURAL_EXPR = new Function( + "n", + `return (${catalog.plural_expr})` + ); + Documentation.LOCALE = catalog.locale; + }, + + /** + * helper function to focus on search bar + */ + focusSearchBar: () => { + document.querySelectorAll("input[name=q]")[0]?.focus(); + }, + + /** + * Initialise the domain index toggle buttons + */ + initDomainIndexTable: () => { + const toggler = (el) => { + const idNumber = el.id.substr(7); + const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`); + if (el.src.substr(-9) === "minus.png") { + el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`; + toggledRows.forEach((el) => (el.style.display = "none")); + } else { + el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`; + toggledRows.forEach((el) => (el.style.display = "")); + } + }; + + const togglerElements = document.querySelectorAll("img.toggler"); + togglerElements.forEach((el) => + el.addEventListener("click", (event) => toggler(event.currentTarget)) + ); + togglerElements.forEach((el) => (el.style.display = "")); + if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler); + }, + + initOnKeyListeners: () => { + // only install a listener if it is really needed + if ( + !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS && + !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS + ) + return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.altKey || event.ctrlKey || event.metaKey) return; + + if (!event.shiftKey) { + switch (event.key) { + case "ArrowLeft": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const prevLink = document.querySelector('link[rel="prev"]'); + if (prevLink && prevLink.href) { + window.location.href = prevLink.href; + event.preventDefault(); + } + break; + case "ArrowRight": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const nextLink = document.querySelector('link[rel="next"]'); + if (nextLink && nextLink.href) { + window.location.href = nextLink.href; + event.preventDefault(); + } + break; + } + } + + // some keyboard layouts may need Shift to get / + switch (event.key) { + case "/": + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break; + Documentation.focusSearchBar(); + event.preventDefault(); + } + }); + }, +}; + +// quick alias for translations +const _ = Documentation.gettext; + +_ready(Documentation.init); diff --git a/_static/documentation_options.js b/_static/documentation_options.js new file mode 100644 index 0000000..cf359c0 --- /dev/null +++ b/_static/documentation_options.js @@ -0,0 +1,14 @@ +var DOCUMENTATION_OPTIONS = { + URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), + VERSION: '0.1', + LANGUAGE: 'en', + COLLAPSE_INDEX: false, + BUILDER: 'html', + FILE_SUFFIX: '.html', + LINK_SUFFIX: '.html', + HAS_SOURCE: true, + SOURCELINK_SUFFIX: '.txt', + NAVIGATION_WITH_KEYS: false, + SHOW_SEARCH_SUMMARY: true, + ENABLE_SEARCH_SHORTCUTS: true, +}; \ No newline at end of file diff --git a/_static/file.png b/_static/file.png new file mode 100644 index 0000000000000000000000000000000000000000..a858a410e4faa62ce324d814e4b816fff83a6fb3 GIT binary patch literal 286 zcmV+(0pb3MP)s`hMrGg#P~ix$^RISR_I47Y|r1 z_CyJOe}D1){SET-^Amu_i71Lt6eYfZjRyw@I6OQAIXXHDfiX^GbOlHe=Ae4>0m)d(f|Me07*qoM6N<$f}vM^LjV8( literal 0 HcmV?d00001 diff --git a/_static/language_data.js b/_static/language_data.js new file mode 100644 index 0000000..250f566 --- /dev/null +++ b/_static/language_data.js @@ -0,0 +1,199 @@ +/* + * language_data.js + * ~~~~~~~~~~~~~~~~ + * + * This script contains the language-specific data used by searchtools.js, + * namely the list of stopwords, stemmer, scorer and splitter. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; + + +/* Non-minified version is copied as a separate JS file, is available */ + +/** + * Porter Stemmer + */ +var Stemmer = function() { + + var step2list = { + ational: 'ate', + tional: 'tion', + enci: 'ence', + anci: 'ance', + izer: 'ize', + bli: 'ble', + alli: 'al', + entli: 'ent', + eli: 'e', + ousli: 'ous', + ization: 'ize', + ation: 'ate', + ator: 'ate', + alism: 'al', + iveness: 'ive', + fulness: 'ful', + ousness: 'ous', + aliti: 'al', + iviti: 'ive', + biliti: 'ble', + logi: 'log' + }; + + var step3list = { + icate: 'ic', + ative: '', + alize: 'al', + iciti: 'ic', + ical: 'ic', + ful: '', + ness: '' + }; + + var c = "[^aeiou]"; // consonant + var v = "[aeiouy]"; // vowel + var C = c + "[^aeiouy]*"; // consonant sequence + var V = v + "[aeiou]*"; // vowel sequence + + var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 + var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + diff --git a/_static/minus.png b/_static/minus.png new file mode 100644 index 0000000000000000000000000000000000000000..d96755fdaf8bb2214971e0db9c1fd3077d7c419d GIT binary patch literal 90 zcmeAS@N?(olHy`uVBq!ia0vp^+#t*WBp7;*Yy1LIik>cxAr*|t7R?Mi>2?kWtu=nj kDsEF_5m^0CR;1wuP-*O&G^0G}KYk!hp00i_>zopr08q^qX#fBK literal 0 HcmV?d00001 diff --git a/_static/plus.png b/_static/plus.png new file mode 100644 index 0000000000000000000000000000000000000000..7107cec93a979b9a5f64843235a16651d563ce2d GIT binary patch literal 90 zcmeAS@N?(olHy`uVBq!ia0vp^+#t*WBp7;*Yy1LIik>cxAr*|t7R?Mi>2?kWtu>-2 m3q%Vub%g%s<8sJhVPMczOq}xhg9DJoz~JfX=d#Wzp$Pyb1r*Kz literal 0 HcmV?d00001 diff --git a/_static/pygments.css b/_static/pygments.css new file mode 100644 index 0000000..6110e9f --- /dev/null +++ b/_static/pygments.css @@ -0,0 +1,84 @@ +pre { line-height: 125%; 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font-weight: bold } /* Literal.Number.Integer.Long */ \ No newline at end of file diff --git a/_static/searchtools.js b/_static/searchtools.js new file mode 100644 index 0000000..97d56a7 --- /dev/null +++ b/_static/searchtools.js @@ -0,0 +1,566 @@ +/* + * searchtools.js + * ~~~~~~~~~~~~~~~~ + * + * Sphinx JavaScript utilities for the full-text search. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = docUrlRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = docUrlRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/_static/sphinx_highlight.js b/_static/sphinx_highlight.js new file mode 100644 index 0000000..aae669d --- /dev/null +++ b/_static/sphinx_highlight.js @@ -0,0 +1,144 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + parent.insertBefore( + span, + parent.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(SphinxHighlight.highlightSearchWords); +_ready(SphinxHighlight.initEscapeListener); diff --git a/cpg.html b/cpg.html new file mode 100644 index 0000000..58b7389 --- /dev/null +++ b/cpg.html @@ -0,0 +1,183 @@ + + + + + + + + CpG Module Documentation — ensembl-anno 0.1 documentation + + + + + + + + + + + + + +
+
+
+ +
+
+
+ +
+

CpG Module Documentation

+

Set of discriminant functions that can recognize structural and compositional features +such as CpG islands, promoter regions and first splice-donor sites. +Davuluri RV, Grosse I, Zhang MQ: Computational identification of promoters and +first exons in the human genome. Nat Genet. 2001, 29(4):412-417. [PMID: 11726928]

+
+
+ensembl.tools.anno.simple_feature_annotation.cpg.run_cpg(genome_file: PathLike, output_dir: Path, cpg_bin: Path = PosixPath('cpg_lh'), cpg_min_length: int = 400, cpg_min_gc_content: int = 50, cpg_min_oe: float = 0.6, num_threads: int = 1) → None[source]
+

Run CpG islands on genomic slices

+
+
+
param genome_file:
+

Genome file path.

+
+
type genome_file:
+

PathLike

+
+
param output_dir:
+

Working directory path

+
+
type output_dir:
+

Path

+
+
param cpg_bin:
+

CpG software path.

+
+
type cpg_bin:
+

Path

+
+
param cpg_min_length:
+

Min length of CpG islands

+
+
type cpg_min_length:
+

int

+
+
param cpg_min_gc_content:
+

Min GC frequency percentage

+
+
type cpg_min_gc_content:
+

int

+
+
param cpg_min_oe:
+

Min ratio of the observed to expected number of CpG (CpGo/e)

+
+
type cpg_min_oe:
+

float

+
+
param num_threads:
+

int, number of threads.

+
+
type num_threads:
+

int

+
+
return:
+

None

+
+
rtype:
+

None

+
+
+
+
+ +
+ + +
+
+
+
+
+
+ +

Table of Contents

+

Index

+ + +
+

Search

+
+ + +
+
+ +
+
+
+
+ +
+
+
+
+ previous | + next | + modules | + index +
+
+
+ Show Source +
+
+ +
+ + +
+
+
+
+ + + \ No newline at end of file diff --git a/doctrees/cpg.doctree b/doctrees/cpg.doctree new file mode 100644 index 0000000000000000000000000000000000000000..d1a7c987acf6b5b88164404e9a1d68c9af1f1499 GIT binary patch literal 20286 zcmeHPdyFKL^VKW_JS?_pc#3vC(a_Q>w+-Er|_bG8$m#VK5F<6KCHOiZhHre?cm zd%DN{xZ90zf@Ms6N=XR0qhNuFgpz=Qz=4P$#2*lehY~;p@%kemKqNr|i9bMqECs~x ztLp0Nnd#~6-bj&*u(ZDE>Z-54@Ao~by6UU?@u^RK|9i*8e|$OY*^am0uv#t8Z?Q1p zvn{_FcbOL@uOt^-|vV@PJM$>lOR=~XE*@Q1q^~iC&8vL6}!xMD(%@4?Wql#O#TqtCtgZwzLZEl zr+XH-iV}N;&zYGR_5`0!x!>lKuH&&}JKnMQycI=(vlB;4 znHRF|j=N!bp5OlfX2VU%r5F;{ZN0xtt8wZYY>x1jY^}vTo8}D8>p0O>U zar1p!#x?XEOFg4+rv;;N+D=m_o`h2UiH_!FM{J)uc07p23_I>Zwq54I&Kt%yWWCNj z7B!5^7cX8~H!eT6cICp>l}nd5u3UPgVf@I`H{bo#mT~FQBbOh3?DC^9Rr2pM{}1DL z2xA)j;9&2Pk!M?&tu-<{kUu_YpR=DpfEibQ2|I7dXs^Qc$oBo=Wjcg+A*AykK%_Gf zFV-#?YcLQQGiv+X1w^X4ai)>>oD|2KFT7dejg~{ioiRR%0lAqAIcgjo!>EflX6Rtt zp^%-c!@sWdARW_eJ1*NYKI(^!r>)3-kF&?t4L^?H`ew@s@TP}i*Vz%T*9~aU+;O~t 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z-(rU@WQ8irBq~~$`mC4i1KkGlIzGK%2V7>2(9(j?ZAMI`uh9xjg-NIh3h13X@@`2y z*!jU7k^XzI+-b5f3_=qXg?*2q0Cbs1MP`t1W>-xGlqCTr<>x1QCO{1TmAqp^!kwP| zV7X&rGCxH;L=Y5mJ!4PQ@tpK5e?PJI86-~m*yE@(=5IriEC~B%pV4c6prJz6J-!S- z8z9RGiMV}OD3X4MC=%lvRuTth(Zr7P*DKQK{mgi)v1A*wK$sm~NvV&kQvi}K7MBv_~wi>#hUjAT@nM}}xVu&&99ki2k@cW%O9!K5XT{K4>SytN#!u{QppQVw40E{$|J%xH= zQD())I~T4z3VCjX1C$7tz*9>B{$T|k&T5g#9Pen(5Y#o{o3gSHc!G0ILfJ}c~yahG0$Dpqv#b3M)HNC*L zP*F>D+~;ivB}+CGFZ~Tt79zyxgJg^tPG#+)Ry~UYcVIn%?fL`QfC>z!DO5yBZ(^J~ zBIES}OL`+!m>;CDnNg4R;lf8C!C|Ndxx>%e7(eo zWLUeyPcZ)$RjTt<8BXB8FhwjvB7h3lM8}=Tc_)g_ML$-zCy=LG&R#)GW#;qh z^e4n4h0=48B{#ylm%c`Oj7OJg+I=b?7*8VyS;nV4hhzGdbLu7$nMeqQLFb}1r=C!<881b6x+g{Qqr`ad( RL;@MnJ`0SraY=fe{{<|}!KDBI literal 0 HcmV?d00001 diff --git a/dust.html b/dust.html new file mode 100644 index 0000000..125fe2d --- /dev/null +++ b/dust.html @@ -0,0 +1,165 @@ + + + + + + + + DustMasker Module Documentation — ensembl-anno 0.1 documentation + + + + + + + + + + + + + +
+
+
+ +
+
+
+ +
+

DustMasker Module Documentation

+

DustMasker is a program that identifies and masks out low complexity +parts of a genome using a new and improved DUST algorithm.

+

Morgulis A, Gertz EM, Schaffer AA, Agarwala R. A Fast and Symmetric +DUST Implementation to Mask Low-Complexity DNA Sequences.

+
+
+ensembl.tools.anno.repeat_annotation.dust.run_dust(genome_file: PathLike, output_dir: Path, dust_bin: Path = PosixPath('dustmasker'), num_threads: int = 1) → None[source]
+
+
Run Dust on genomic slices with mutiprocessing
+
param genome_file:
+

Genome file path.

+
+
type genome_file:
+

PathLike

+
+
param output_dir:
+

Working directory path.

+
+
type output_dir:
+

Path

+
+
param dust_bin:
+

Dust software path.

+
+
type dust_bin:
+

Path, default dustmasker

+
+
param num_threads:
+

Number of threads.

+
+
type num_threads:
+

int, default 1

+
+
return:
+

None

+
+
rtype:
+

None

+
+
+
+
+
+ +
+ + +
+
+
+
+
+
+ +

Table of Contents

+

Index

+ + +
+

Search

+
+ + +
+
+ +
+
+
+
+ +
+
+
+
+ previous | + next | + modules | + index +
+
+
+ Show Source +
+
+ +
+ + +
+
+
+
+ + + \ No newline at end of file diff --git a/eponine.html b/eponine.html new file mode 100644 index 0000000..cd0198a --- /dev/null +++ b/eponine.html @@ -0,0 +1,172 @@ + + + + + + + + Eponine Module Documentation — ensembl-anno 0.1 documentation + + + + + + + + + + + + + +
+
+
+ +
+
+
+ +
+

Eponine Module Documentation

+

Eponine is a probabilistic method for detecting transcription start sites (TSS) +in mammalian genomic sequence, with good specificity and excellent positional accuracy. +Down TA, Hubbard TJ. Computational detection and location of transcription start sites +in mammalian genomic DNA. Genome Res. 2002 Mar;12(3):458-61. doi: 10.1101/gr.216102. +PMID: 11875034; PMCID: PMC155284.

+
+
+ensembl.tools.anno.simple_feature_annotation.eponine.run_eponine(genome_file: PathLike, output_dir: Path, num_threads: int = 1, java_bin: Path = PosixPath('java'), eponine_bin: Path = PosixPath('/hps/software/users/ensembl/ensw/C8-MAR21-sandybridge/linuxbrew/opt/eponine/libexec/eponine-scan.jar'), eponine_threshold: float = 0.999) → None[source]
+
+
Run Eponine on genomic slices
+
param genome_file:
+

Genome file path.

+
+
param genome_file:
+

PathLike

+
+
param output_dir:
+

Working directory path.

+
+
param output_dir:
+

Path

+
+
param java_bin:
+

Java path.

+
+
param java_bin:
+

Path, default java

+
+
param eponine_bin:
+

Eponine software path

+
+
param eponine_bin:
+

Path

+
+
param num_threads:
+

Number of threads.

+
+
param num_threads:
+

int, default 1

+
+
return:
+

None

+
+
rtype:
+

None

+
+
+
+
+
+ +
+ + +
+
+
+
+
+
+ +

Table of Contents

+

Index

+ + +
+

Search

+
+ + +
+
+ +
+
+
+
+ +
+
+
+
+ previous | + next | + modules | + index +
+
+
+ Show Source +
+
+ +
+ + +
+
+
+
+ + + \ No newline at end of file diff --git a/genblast.html b/genblast.html new file mode 100644 index 0000000..b6493b4 --- /dev/null +++ b/genblast.html @@ -0,0 +1,218 @@ + + + + + + + + Genblast Module Documentation — ensembl-anno 0.1 documentation + + + + + + + + + + + + + +
+
+
+ +
+
+
+ +
+

Genblast Module Documentation

+

GenBlast identifies homologous gene sequences in genomic databases. +One of the key features of GenBlast is its flexibility to handle +comparative genomics tasks and accurately identify homologs even when +the sequences have undergone significant evolutionary changes. +This capability makes it a valuable resource for researchers studying gene +evolution, gene families, and gene function across diverse species. +GenBlast has been widely used in various genomic analyses and is available as +a standalone command-line tool or as part of different bioinformatics pipelines. +Researchers in the field of comparative genomics and gene function analysis +often rely on GenBlast to perform sensitive homology searches and obtain +valuable insights into the evolutionary relationships and functional conservation +of genes in different organisms.

+

She, R., Chu, J.S., Uyar, B., Wang, J., Wang, K., and Chen, N. (2011). +GenBlastA: enabling BLAST to identify homologous gene sequences. +Genome Res., 21(5): 936-949.

+
+
+ensembl.tools.anno.protein_annotation.genblast.run_genblast(masked_genome: Path, output_dir: Path, protein_dataset: Path, max_intron_length: int, genblast_timeout_secs: int = 10800, genblast_bin: Path = PosixPath('genblast'), convert2blastmask_bin: Path = PosixPath('convert2blastmask'), makeblastdb_bin: Path = PosixPath('makeblastdb'), num_threads: int = 1, protein_set: str = ['uniprot', 'orthodb']) → None[source]
+

Executes GenBlast on genomic slices

+
+
+
param masked_genome:
+

Masked genome file path.

+
+
type masked_genome:
+

Path

+
+
param output_dir:
+

Working directory path.

+
+
type output_dir:
+

Path

+
+
param protein_dataset:
+

Protein dataset (Uniprot/OrthoDb) path.

+
+
type protein_dataset:
+

Path

+
+
param genblast_timeout_secs:
+

Time for timeout (sec).

+
+
type genblast_timeout_secs:
+

int, default 10800

+
+
param max_intron_length:
+

Maximum intron length.

+
+
type max_intron_length:
+

int

+
+
param genblast_bin:
+

Software path.

+
+
type genblast_bin:
+

Path, default genblast

+
+
param convert2blastmask_bin:
+

Software path.

+
+
type convert2blastmask_bin:
+

Path, default convert2blastmask

+
+
param makeblastdb_bin:
+

Software path.

+
+
type makeblastdb_bin:
+

Path, default makeblastdb

+
+
param genblast_timeout:
+

seconds

+
+
type genblast_timeout:
+

int, default 1

+
+
param num_threads:
+

int, number of threads.

+
+
type num_threads:
+

int, default 1

+
+
param protein_set:
+

Source

+
+
type str:
+

[“uniprot”, “orthodb”]

+
+
return:
+

None

+
+
rtype:
+

None

+
+
+
+
+ +
+ + +
+
+
+
+
+
+ +

Table of Contents

+

Index

+ + +
+

Search

+
+ + +
+
+ +
+
+
+
+ +
+
+
+
+ previous | + next | + modules | + index +
+
+
+ Show Source +
+
+ +
+ + +
+
+
+
+ + + \ No newline at end of file diff --git a/genindex.html b/genindex.html new file mode 100644 index 0000000..b2cac20 --- /dev/null +++ b/genindex.html @@ -0,0 +1,281 @@ + + + + + + + Index — ensembl-anno 0.1 documentation + + + + + + + + + + + +
+
+
+ +
+
+
+ + +

Index

+ +
+ E + | M + | R + | S + +
+

E

+ + + +
    +
  • + ensembl.tools.anno.protein_annotation.genblast + +
    • +
  • + ensembl.tools.anno.repeat_annotation.dust + +
    • +
  • + ensembl.tools.anno.repeat_annotation.red + +
    • +
  • + ensembl.tools.anno.repeat_annotation.repeatmasker + +
    • +
  • + ensembl.tools.anno.repeat_annotation.trf + +
    • +
  • + ensembl.tools.anno.simple_feature_annotation.cpg + +
    • +
    +
  • + ensembl.tools.anno.simple_feature_annotation.eponine + +
    • +
  • + ensembl.tools.anno.snc_rna_annotation.trnascan + +
    • +
  • + ensembl.tools.anno.transcriptomic_annotation.minimap + +
    • +
  • + ensembl.tools.anno.transcriptomic_annotation.scallop + +
    • +
  • + ensembl.tools.anno.transcriptomic_annotation.star + +
    • +
  • + ensembl.tools.anno.transcriptomic_annotation.stringtie + +
    • +
+ +

M

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+
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Ensembl-anno

+

Anno tool kit

+
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Contents

+

Check out installation section for further information on how +to install the project.

+
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Index

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Indices and tables

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+
+
+ +
+
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+ +
+

API Setup and installation

+
+

Requirements

+

An Ensembl API checkout including:

+ +
+

Software

+
    +

  1. Python 3.8+

    2. +

  2. Bioperl 1.6.9+

    3. +
+
+
+

Python Modules

+
    +

  1. argschema

    2. +
+
+
+
+

Installation

+

Directly from GitHub:

+
1git clone https://github.com/Ensembl/ensembl-analysis -b experimental/gbiab
+2git clone https://github.com/Ensembl/ensembl-production
+3git clone https://github.com/Ensembl/ensembl-hive
+4git clone https://github.com/Ensembl/ensembl-taxonomy
+5git clone https://github.com/Ensembl/ensembl-orm
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+ + + \ No newline at end of file diff --git a/minimap.html b/minimap.html new file mode 100644 index 0000000..6965c6d --- /dev/null +++ b/minimap.html @@ -0,0 +1,184 @@ + + + + + + + + Minimap2 Module Documentation — ensembl-anno 0.1 documentation + + + + + + + + + + + + + +
+
+
+ +
+
+
+ +
+

Minimap2 Module Documentation

+

Minimap2 is a pairwise sequence alignment algorithm designed for efficiently comparing nucleotide sequences. +The algorithm uses a versatile indexing strategy to quickly find approximate matches between sequences, +allowing it to efficiently align long sequences against reference genomes or other sequences.

+

Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34(18), 3094-3100.

+
+
+ensembl.tools.anno.transcriptomic_annotation.minimap.run_minimap2(output_dir: Path, long_read_fastq_dir: Path, genome_file: Path, minimap2_bin: Path = PosixPath('minimap2'), paftools_bin: Path = PosixPath('paftools.js'), max_intron_length: int = 100000, num_threads: int = 1) → None[source]
+

Run Minimap2 to align long read data against genome file. +Default Minimap set for PacBio data.

+
+
+
param output_dir:
+

Working directory path.

+
+
type output_dir:
+

Path

+
+
param long_read_fastq_dir:
+

Long read directory path.

+
+
type long_read_fastq_dir:
+

Path

+
+
param genome_file:
+

Genome file path.

+
+
type genome_file:
+

Path

+
+
param minimap2_bin:
+

Software path.

+
+
type minimap2_bin:
+

Path, default minimap2

+
+
param paftools_bin:
+

Software path.

+
+
type paftools_bin:
+

Path, default paftools.js

+
+
param max_intron_length:
+

The maximum intron size for alignments. Defaults to 100000.

+
+
type max_intron_length:
+

int, default 100000

+
+
param num_threads:
+

Number of available threads.

+
+
type num_threads:
+

int, default 1

+
+
return:
+

None

+
+
rtype:
+

None

+
+
+
+
+ +
+ + +
+
+
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+
+ +

Table of Contents

+

Index

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Search

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Python Module Index

+ +
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+ e
+ ensembl +
    + ensembl.tools.anno.protein_annotation.genblast +
    + ensembl.tools.anno.repeat_annotation.dust +
    + ensembl.tools.anno.repeat_annotation.red +
    + ensembl.tools.anno.repeat_annotation.repeatmasker +
    + ensembl.tools.anno.repeat_annotation.trf +
    + ensembl.tools.anno.simple_feature_annotation.cpg +
    + ensembl.tools.anno.simple_feature_annotation.eponine +
    + ensembl.tools.anno.snc_rna_annotation.trnascan +
    + ensembl.tools.anno.transcriptomic_annotation.minimap +
    + ensembl.tools.anno.transcriptomic_annotation.scallop +
    + ensembl.tools.anno.transcriptomic_annotation.star +
    + ensembl.tools.anno.transcriptomic_annotation.stringtie +
+ + +
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+ + + \ No newline at end of file diff --git a/red.html b/red.html new file mode 100644 index 0000000..bddc245 --- /dev/null +++ b/red.html @@ -0,0 +1,160 @@ + + + + + + + + Red Module Documentation — ensembl-anno 0.1 documentation + + + + + + + + + + + + + +
+
+
+ +
+
+
+ +
+

Red Module Documentation

+

Red is the first repeat-detection tool capable of labeling its training data +and training itself automatically on an entire genome. +Girgis, H.Z. Red: an intelligent, rapid, accurate tool for detecting repeats +de-novo on the genomic scale. BMC Bioinformatics 16, 227 (2015). +https://doi.org/10.1186/s12859-015-0654-5

+
+
+ensembl.tools.anno.repeat_annotation.red.run_red(genome_file: Path, output_dir: Path, red_bin: Path = PosixPath('Red')) → str[source]
+
+
Run Red on genome file
+
param genome_file:
+

Genome file path.

+
+
type genome_file:
+

Path

+
+
param output_dir:
+

Working directory path.

+
+
type output_dir:
+

Path

+
+
param red_bin:
+

Red software path.

+
+
type red_bin:
+

Path, default Red

+
+
return:
+

Masked genome file

+
+
rtype:
+

str

+
+
+
+
+
+ +
+ + +
+
+
+
+
+
+ +

Table of Contents

+

Index

+ + +
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Search

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+ + + \ No newline at end of file diff --git a/repeatmasker.html b/repeatmasker.html new file mode 100644 index 0000000..8c8c3c2 --- /dev/null +++ b/repeatmasker.html @@ -0,0 +1,182 @@ + + + + + + + + Repeatmasker Module Documentation — ensembl-anno 0.1 documentation + + + + + + + + + + + + + +
+
+
+ +
+
+
+ +
+

Repeatmasker Module Documentation

+

RepeatMasker is a program that screens DNA sequences for interspersed +repeats and low complexity DNA sequences. +Smit, AFA, Hubley, R & Green, P. RepeatMasker Open-4.0

+
+
+ensembl.tools.anno.repeat_annotation.repeatmasker.run_repeatmasker(genome_file: PathLike, output_dir: Path, repeatmasker_bin: Path = PosixPath('RepeatMasker'), library: str = '', repeatmasker_engine: str = 'rmblast', species: str = '', num_threads: int = 1) → None[source]
+

Executes RepeatMasker on the genome slices and stores the final annotation.gtf in repeatmasker_output

+
+
+
param genome_file:
+

Genome file path.

+
+
type genome_file:
+

PathLike

+
+
param output_dir:
+

Output directory path.

+
+
type output_dir:
+

Path

+
+
param repeatmasker_bin:
+

RepeatMasker executable path.

+
+
type repeatmasker_bin:
+

Path, default RepeatMasker

+
+
param library:
+

Custom repeat library.

+
+
type library:
+

str

+
+
param repeatmasker_engine:
+

RepeatMasker engine.

+
+
type repeatmasker_engine:
+

str, default rmblast

+
+
param species:
+

Species name.

+
+
type species:
+

str

+
+
param num_threads:
+

Number of threads.

+
+
type num_threads:
+

int, default 1

+
+
return:
+

None

+
+
rtype:
+

None

+
+
+
+
+ +
+ + +
+
+
+
+
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+ +

Table of Contents

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Index

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+ + + \ No newline at end of file diff --git a/scallop.html b/scallop.html new file mode 100644 index 0000000..b947e84 --- /dev/null +++ b/scallop.html @@ -0,0 +1,177 @@ + + + + + + + + Scallop Module Documentation — ensembl-anno 0.1 documentation + + + + + + + + + + + + + +
+
+
+ +
+
+
+ +
+

Scallop Module Documentation

+

Scallop is a high-performance tool designed for the accurate and efficient quantification +of transcriptome assembly. +It’s capable of handling large-scale transcriptomic data while providing precise estimates +of transcript abundances. +Scallop’s algorithmic approach allows it to efficiently reconstruct transcript structures +and quantify their expression levels, making it a valuable resource for studying gene +expression and transcriptome analysis.

+

Shao M, Kingsford C. Accurate assembly of transcripts through phase-preserving graph +decomposition. Nat Biotechnol. +2017 Dec;35(12):1167-1169. doi: 10.1038/nbt.4020. Epub 2017 Nov 13. PMID: 29131147; PMCID: PMC5722698.

+
+
+ensembl.tools.anno.transcriptomic_annotation.scallop.run_scallop(output_dir: Path, scallop_bin: Path = PosixPath('scallop'), prlimit_bin: Path = PosixPath('prlimit'), stringtie_bin: Path = PosixPath('stringtie'), memory_limit: int = 42949672960) → None[source]
+

Run Scallop assembler on short read data after STAR alignment.

+
+
+
param output_dir:
+

Working directory path.

+
+
type output_dir:
+

Path

+
+
param scallop_bin:
+

Software path.

+
+
type scallop_bin:
+

Path, default scallop

+
+
param prlimit_bin:
+

Software path.

+
+
type prlimit_bin:
+

Path, default prlimit

+
+
param stringtie_bin:
+

Software path.

+
+
type stringtie_bin:
+

Path, default stringtie

+
+
param memory_limit:
+

Memory limit Scallop command Defaults to 40*1024**3.

+
+
type memory_limit:
+

int

+
+
return:
+

None

+
+
rtype:
+

None

+
+
+
+
+ +
+ + +
+
+
+
+
+
+ +

Table of Contents

+

Index

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+ + + \ No newline at end of file diff --git a/searchindex.js b/searchindex.js new file mode 100644 index 0000000..0a03cc6 --- /dev/null +++ b/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"docnames": ["cpg", "dust", "eponine", "genblast", "index", "install", "license", "minimap", "red", "repeatmasker", "scallop", "star", "stringtie", "trf", "trnascan"], "filenames": ["cpg.rst", "dust.rst", "eponine.rst", "genblast.rst", "index.rst", "install.rst", "license.rst", "minimap.rst", "red.rst", "repeatmasker.rst", "scallop.rst", "star.rst", "stringtie.rst", "trf.rst", "trnascan.rst"], "titles": ["CpG Module Documentation", "DustMasker Module Documentation", "Eponine Module Documentation", "Genblast Module Documentation", "Ensembl-anno", "API Setup and installation", "License", "Minimap2 Module Documentation", "Red Module Documentation", "Repeatmasker Module Documentation", "Scallop Module Documentation", "STAR Module Documentation", "Stringtie Module Documentation", "TRF Module 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11, "stringti": 12, "trf": 13, "trnascan": 14, "se": 14}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1, "sphinx": 58}, "alltitles": {"CpG Module Documentation": [[0, "module-ensembl.tools.anno.simple_feature_annotation.cpg"]], "DustMasker Module Documentation": [[1, "module-ensembl.tools.anno.repeat_annotation.dust"]], "Eponine Module Documentation": [[2, "module-ensembl.tools.anno.simple_feature_annotation.eponine"]], "Genblast Module Documentation": [[3, "module-ensembl.tools.anno.protein_annotation.genblast"]], "Ensembl-anno": [[4, "ensembl-anno"]], "Contents": [[4, "contents"]], "Index": [[4, null]], "Indices and tables": [[4, "indices-and-tables"]], "API Setup and installation": [[5, "api-setup-and-installation"]], "Requirements": [[5, "requirements"]], "Software": [[5, "software"]], "Python Modules": [[5, "python-modules"]], "Installation": [[5, "installation"]], "License": [[6, "license"]], "Minimap2 Module Documentation": [[7, "module-ensembl.tools.anno.transcriptomic_annotation.minimap"]], "Red Module Documentation": [[8, "module-ensembl.tools.anno.repeat_annotation.red"]], "Repeatmasker Module Documentation": [[9, "module-ensembl.tools.anno.repeat_annotation.repeatmasker"]], "Scallop Module Documentation": [[10, "module-ensembl.tools.anno.transcriptomic_annotation.scallop"]], "STAR Module Documentation": [[11, "module-ensembl.tools.anno.transcriptomic_annotation.star"]], "Stringtie Module Documentation": [[12, "module-ensembl.tools.anno.transcriptomic_annotation.stringtie"]], "TRF Module Documentation": [[13, "module-ensembl.tools.anno.repeat_annotation.trf"]], "tRNAscan-SE Module Documentation": [[14, "module-ensembl.tools.anno.snc_rna_annotation.trnascan"]]}, "indexentries": {"ensembl.tools.anno.simple_feature_annotation.cpg": [[0, "module-ensembl.tools.anno.simple_feature_annotation.cpg"]], "module": [[0, "module-ensembl.tools.anno.simple_feature_annotation.cpg"], [1, "module-ensembl.tools.anno.repeat_annotation.dust"], [2, "module-ensembl.tools.anno.simple_feature_annotation.eponine"], [3, "module-ensembl.tools.anno.protein_annotation.genblast"], [7, "module-ensembl.tools.anno.transcriptomic_annotation.minimap"], [8, "module-ensembl.tools.anno.repeat_annotation.red"], [9, "module-ensembl.tools.anno.repeat_annotation.repeatmasker"], [10, "module-ensembl.tools.anno.transcriptomic_annotation.scallop"], [11, "module-ensembl.tools.anno.transcriptomic_annotation.star"], [12, "module-ensembl.tools.anno.transcriptomic_annotation.stringtie"], [13, "module-ensembl.tools.anno.repeat_annotation.trf"], [14, "module-ensembl.tools.anno.snc_rna_annotation.trnascan"]], "run_cpg() (in module ensembl.tools.anno.simple_feature_annotation.cpg)": [[0, "ensembl.tools.anno.simple_feature_annotation.cpg.run_cpg"]], "ensembl.tools.anno.repeat_annotation.dust": [[1, "module-ensembl.tools.anno.repeat_annotation.dust"]], "run_dust() (in module ensembl.tools.anno.repeat_annotation.dust)": [[1, "ensembl.tools.anno.repeat_annotation.dust.run_dust"]], "ensembl.tools.anno.simple_feature_annotation.eponine": [[2, "module-ensembl.tools.anno.simple_feature_annotation.eponine"]], "run_eponine() (in module ensembl.tools.anno.simple_feature_annotation.eponine)": [[2, "ensembl.tools.anno.simple_feature_annotation.eponine.run_eponine"]], "ensembl.tools.anno.protein_annotation.genblast": [[3, "module-ensembl.tools.anno.protein_annotation.genblast"]], "run_genblast() (in module ensembl.tools.anno.protein_annotation.genblast)": [[3, "ensembl.tools.anno.protein_annotation.genblast.run_genblast"]], "ensembl.tools.anno.transcriptomic_annotation.minimap": [[7, "module-ensembl.tools.anno.transcriptomic_annotation.minimap"]], "run_minimap2() (in module ensembl.tools.anno.transcriptomic_annotation.minimap)": [[7, "ensembl.tools.anno.transcriptomic_annotation.minimap.run_minimap2"]], "ensembl.tools.anno.repeat_annotation.red": [[8, "module-ensembl.tools.anno.repeat_annotation.red"]], "run_red() (in module ensembl.tools.anno.repeat_annotation.red)": [[8, "ensembl.tools.anno.repeat_annotation.red.run_red"]], "ensembl.tools.anno.repeat_annotation.repeatmasker": [[9, "module-ensembl.tools.anno.repeat_annotation.repeatmasker"]], "run_repeatmasker() (in module ensembl.tools.anno.repeat_annotation.repeatmasker)": [[9, "ensembl.tools.anno.repeat_annotation.repeatmasker.run_repeatmasker"]], "ensembl.tools.anno.transcriptomic_annotation.scallop": [[10, "module-ensembl.tools.anno.transcriptomic_annotation.scallop"]], "run_scallop() (in module ensembl.tools.anno.transcriptomic_annotation.scallop)": [[10, "ensembl.tools.anno.transcriptomic_annotation.scallop.run_scallop"]], "ensembl.tools.anno.transcriptomic_annotation.star": [[11, "module-ensembl.tools.anno.transcriptomic_annotation.star"]], "run_star() (in module ensembl.tools.anno.transcriptomic_annotation.star)": [[11, "ensembl.tools.anno.transcriptomic_annotation.star.run_star"]], "subsample_transcriptomic_data() (in module ensembl.tools.anno.transcriptomic_annotation.star)": [[11, "ensembl.tools.anno.transcriptomic_annotation.star.subsample_transcriptomic_data"]], "ensembl.tools.anno.transcriptomic_annotation.stringtie": [[12, "module-ensembl.tools.anno.transcriptomic_annotation.stringtie"]], "run_stringtie() (in module ensembl.tools.anno.transcriptomic_annotation.stringtie)": [[12, "ensembl.tools.anno.transcriptomic_annotation.stringtie.run_stringtie"]], "ensembl.tools.anno.repeat_annotation.trf": [[13, "module-ensembl.tools.anno.repeat_annotation.trf"]], "run_trf() (in module ensembl.tools.anno.repeat_annotation.trf)": [[13, "ensembl.tools.anno.repeat_annotation.trf.run_trf"]], "ensembl.tools.anno.snc_rna_annotation.trnascan": [[14, "module-ensembl.tools.anno.snc_rna_annotation.trnascan"]], "run_trnascan() (in module ensembl.tools.anno.snc_rna_annotation.trnascan)": [[14, "ensembl.tools.anno.snc_rna_annotation.trnascan.run_trnascan"]]}}) \ No newline at end of file diff --git a/star.html b/star.html new file mode 100644 index 0000000..f3ea268 --- /dev/null +++ b/star.html @@ -0,0 +1,221 @@ + + + + + + + + STAR Module Documentation — ensembl-anno 0.1 documentation + + + + + + + + + + + + + +
+
+
+ +
+
+
+ +
+

STAR Module Documentation

+

The STAR (Spliced Transcripts Alignment to a Reference) alignment tool is widely used +in genomics research for aligning RNA-seq data to a reference genome. +Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. +Bioinformatics. 2013;29(1):15-21. doi:10.1093/bioinformatics/bts635

+
+
+ensembl.tools.anno.transcriptomic_annotation.star.run_star(genome_file: Path, output_dir: Path, short_read_fastq_dir: Path, delete_pre_trim_fastq: bool = False, trim_fastq: bool = False, max_reads_per_sample: int = 0, max_intron_length: int = 100000, num_threads: int = 1, star_bin: Path = PosixPath('star'), samtools_bin: Path = PosixPath('samtools'), trim_galore_bin: Path = PosixPath('trim_galore')) → None[source]
+
+
Run STAR alignment on list of short read data.
+
param genome_file:
+

Genome file path.

+
+
type genome_file:
+

Path

+
+
param output_dir:
+

Working directory path.

+
+
type output_dir:
+

Path

+
+
param short_read_fastq_dir:
+

Short read directory path.

+
+
type short_read_fastq_dir:
+

Path

+
+
param delete_pre_trim_fastq:
+

Delete the original fastq files after trimming. Defaults to False.

+
+
type delete_pre_trim_fastq:
+

boolean, default False

+
+
param trim_fastq:
+

Trim short read files using TrimGalore. Defaults to False.

+
+
type trim_fastq:
+

boolean, default False

+
+
param max_reads_per_sample:
+

Max number of reads per sample. Defaults to 0 (unlimited).

+
+
type max_reads_per_sample:
+

int, default 0

+
+
param max_intron_length:
+

The maximum intron size for alignments. Defaults to 100000.

+
+
type max_intron_length:
+

int, default 100000

+
+
param num_threads:
+

Number of available threads.

+
+
type num_threads:
+

int, default 1

+
+
param star_bin:
+

Software path.

+
+
type star_bin:
+

Path, default star

+
+
param samtools_bin:
+

Software path.

+
+
type samtools_bin:
+

Path,default samtools

+
+
param trim_galore_bin:
+

Software path.

+
+
type trim_galore_bin:
+

Path, default trim_galore

+
+
return:
+

None

+
+
rtype:
+

None

+
+
+
+
+
+ +
+
+ensembl.tools.anno.transcriptomic_annotation.star.subsample_transcriptomic_data(fastq_file_list: List[Path], num_threads: int = 2) → None[source]
+

Subsample paired fastq files.

+
+
Parameters:
+
    +

  • fastq_file_list – List of fastq file path to process.

    • +

  • num_threads – number of threads

    • +
+
+
+
+ +
+ + +
+
+
+
+
+
+ +

Table of Contents

+

Index

+ + +
+

Search

+
+ + +
+
+ +
+
+
+
+ +
+
+
+
+ previous | + next | + modules | + index +
+
+
+ Show Source +
+
+ +
+ + +
+
+
+
+ + + \ No newline at end of file diff --git a/stringtie.html b/stringtie.html new file mode 100644 index 0000000..edc6e83 --- /dev/null +++ b/stringtie.html @@ -0,0 +1,160 @@ + + + + + + + + Stringtie Module Documentation — ensembl-anno 0.1 documentation + + + + + + + + + + + + + +
+
+
+ +
+
+
+ +
+

Stringtie Module Documentation

+

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. +It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and +quantitate full-length transcripts representing multiple splice variants for each gene locus. +Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT & Salzberg SL. StringTie enables improved +reconstruction of a transcriptome from RNA-seq reads Nature Biotechnology 2015, doi:10.1038/nbt.3122

+
+
+ensembl.tools.anno.transcriptomic_annotation.stringtie.run_stringtie(output_dir: Path, stringtie_bin: Path = PosixPath('stringtie'), num_threads: int = 1) → None[source]
+
+
StringTie assembler of short read data.
+
param output_dir:
+

Working directory path.

+
+
type output_dir:
+

Path

+
+
param stringtie_bin:
+

Software path.

+
+
type stringtie_bin:
+

Path, default stringtie

+
+
param num_threads:
+

Number of available threads.

+
+
type num_threads:
+

int, default 1

+
+
return:
+

None

+
+
rtype:
+

None

+
+
+
+
+
+ +
+ + +
+
+
+
+
+
+ +

Table of Contents

+

Index

+ + +
+

Search

+
+ + +
+
+ +
+
+
+
+ +
+
+
+
+ previous | + next | + modules | + index +
+
+
+ Show Source +
+
+ +
+ + +
+
+
+
+ + + \ No newline at end of file diff --git a/trf.html b/trf.html new file mode 100644 index 0000000..820f45c --- /dev/null +++ b/trf.html @@ -0,0 +1,206 @@ + + + + + + + + TRF Module Documentation — ensembl-anno 0.1 documentation + + + + + + + + + + + + + +
+
+
+ +
+
+
+ +
+

TRF Module Documentation

+

Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. +Benson G. Tandem repeats finder: a program to analyze DNA sequences. +Nucleic Acids Res. 1999; 27(2):573–580. doi:10.1093/nar/27.2.573

+
+
+ensembl.tools.anno.repeat_annotation.trf.run_trf(genome_file: PathLike, output_dir: Path, num_threads: int = 1, trf_bin: Path = PosixPath('trf'), match_score: int = 2, mismatch_score: int = 5, delta: int = 7, pm: int = 80, pi: int = 10, minscore: int = 40, maxperiod: int = 500) → None[source]
+
+
Executes TRF on genomic slices
+
param genome_file:
+

Genome file path.

+
+
type genome_file:
+

PathLike

+
+
param output_dir:
+

Working directory path.

+
+
type output_dir:
+

Path

+
+
param num_threads:
+

int, number of threads.

+
+
type num_threads:
+

int, default 1

+
+
param trf_bin:
+

TRF software path.

+
+
type trf_bin:
+

Path, default trf

+
+
param match_score:
+

Matching weight.

+
+
type match_score:
+

int, default 2

+
+
param mismatch_score:
+

Mismatching penalty.

+
+
type mismatch_score:
+

int, default 5

+
+
param delta:
+

Indel penalty.

+
+
type delta:
+

int, default 7

+
+
param pm:
+

Match probability (whole number).

+
+
type pm:
+

int, default 80

+
+
param pi:
+

Indel probability (whole number).

+
+
type pi:
+

int, default 10

+
+
param minscore:
+

Minimum alignment score to report.

+
+
type minscore:
+

int, default 40

+
+
param maxperiod:
+

Maximum period size to report.

+
+
type maxperiod:
+

int, default 500

+
+
return:
+

None

+
+
rtype:
+

None

+
+
+
+
+
+ +
+ + +
+
+
+
+
+
+ +

Table of Contents

+

Index

+ + +
+

Search

+
+ + +
+
+ +
+
+
+
+ +
+
+
+
+ previous | + next | + modules | + index +
+
+
+ Show Source +
+
+ +
+ + +
+
+
+
+ + + \ No newline at end of file diff --git a/trnascan.html b/trnascan.html new file mode 100644 index 0000000..b4c7bc7 --- /dev/null +++ b/trnascan.html @@ -0,0 +1,167 @@ + + + + + + + + tRNAscan-SE Module Documentation — ensembl-anno 0.1 documentation + + + + + + + + + + + + +
+
+
+ +
+
+
+ +
+

tRNAscan-SE Module Documentation

+

tRNAscan-SE identifies 99-100% of transfer RNA genes in DNA sequence while +giving less than one false positive per 15 gigabases. +Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer +RNA genes in genomic sequence. +Nucleic Acids Res. 1997, 25(5):955-64. [PMID: 9023104]

+
+
+ensembl.tools.anno.snc_rna_annotation.trnascan.run_trnascan(genome_file: PathLike, output_dir: Path, trnascan_bin: Path = PosixPath('tRNAscan-SE'), trnascan_filter: Path = PosixPath('EukHighConfidenceFilter'), num_threads: int = 1) → None[source]
+
+
Executes tRNAscan-SE on genomic slices
+
param genome_file:
+

Genome file path.

+
+
type genome_file:
+

PathLike

+
+
param output_dir:
+

working directory path.

+
+
type output_dir:
+

Path

+
+
param trnascan_bin:
+

tRNAscan-SE software path.

+
+
type trnascan_bin:
+

Path, default tRNAscan-SE

+
+
param trnascan_filter:
+

tRNAscan-SE filter set path.

+
+
type trnascan_filter:
+

Path, default EukHighConfidenceFilter

+
+
param num_threads:
+

int, number of threads.

+
+
type num_threads:
+

int, default 1

+
+
return:
+

None

+
+
rtype:
+

None

+
+
+
+
+
+ +
+ + +
+
+
+
+
+
+ +

Table of Contents

+

Index

+ + +
+

Search

+
+ + +
+
+ +
+
+
+
+ +
+
+
+
+ previous | + modules | + index +
+
+
+ Show Source +
+
+ +
+ + +
+
+
+
+ + + \ No newline at end of file