fix tests and filter low entropy fastqs

src/plassembler/__init__.py

@@ -38,6 +38,7 @@
     run_canu,
     run_canu_correct,
     trim_contigs,
+    filter_entropy_fastqs
 )
 from plassembler.utils.run_dnaapler import run_dnaapler
 from plassembler.utils.run_mash import mash_sketch, run_mash
@@ -440,29 +441,37 @@ def run(
         skip_assembly = validate_flye_assembly_info(flye_assembly, flye_info)
 
     if skip_assembly is False:
-        if use_raven is True:
+        logger.info("Running Flye.")
+        run_flye(outdir, threads, raw_flag, pacbio_model, logdir)
+    else:
+        if flye_directory != "nothing":
             logger.info(
-                "You have specified --use_raven. Using Raven for long read assembly."
+                f"You have specified a {flye_directory} with an existing flye assembly."
+            )
+            logger.info("Copying files.")
+            # copies the files to the outdir
+            shutil.copy2(
+                os.path.join(flye_directory, "assembly_info.txt"),
+                os.path.join(outdir, "assembly_info.txt"),
+            )
+            shutil.copy2(
+                os.path.join(flye_directory, "assembly.fasta"),
+                os.path.join(outdir, "assembly.fasta"),
             )
-            logger.info("Running Raven.")
-            run_raven(outdir, threads, logdir)
         else:
-            logger.info("Running Flye.")
-            run_flye(outdir, threads, raw_flag, pacbio_model, logdir)
-    else:
-        logger.info(
-            f"You have specified a {flye_directory} with an existing flye assembly."
-        )
-        logger.info("Copying files.")
-        # copies the files to the outdir
-        shutil.copy2(
-            os.path.join(flye_directory, "assembly_info.txt"),
-            os.path.join(outdir, "assembly_info.txt"),
-        )
-        shutil.copy2(
-            os.path.join(flye_directory, "assembly.fasta"),
-            os.path.join(outdir, "assembly.fasta"),
-        )
+            logger.info(
+                f"You have specified a {flye_assembly} and {flye_info} from an existing flye assembly."
+            )
+            shutil.copy2(
+                flye_assembly,
+                os.path.join(outdir, "assembly.fasta"),
+            )
+            shutil.copy2(
+                flye_info,
+                os.path.join(outdir, "assembly_info.txt"),
+            )
+
+
     # instanatiate the class with some of the commands
     plass = Plass()
     plass.outdir = outdir
@@ -1321,10 +1330,7 @@ def long(
                     corrected_error_rate = 0.045
             else:
                 canu_nano_or_pacbio = "nanopore"
-                if raw_flag is True:  # ont raw
-                    corrected_error_rate = 0.12
-                else:
-                    corrected_error_rate = 0.03
+                corrected_error_rate = 0.12
         else:  # if none by default
             try:
                 float(corrected_error_rate) > 0
@@ -1388,11 +1394,23 @@ def long(
 
             canu_output_dir: Path = Path(outdir) / "canu"
 
+            logger.info(
+                    "Removing junk low entropy reads."
+                )
+
+            # filter entropy of fastq (to remove rubbish repeats) so they don't survive the correction step
+            entropy_filtered_fastq = Path(outdir) / "plasmid_long_entropy_filtered.fastq"
+            filter_entropy_fastqs(plasmidfastqs, entropy_filtered_fastq)
+
+            logger.info(
+                    "Correcting reads with canu prior to running Unicycler."
+                )
+
             try:
                 run_canu_correct(
                     threads,
                     logdir,
-                    plasmidfastqs,
+                    entropy_filtered_fastq,
                     canu_output_dir,
                     canu_nano_or_pacbio,
                     total_flye_plasmid_length,
@@ -1410,7 +1428,7 @@ def long(
                 logger.warning(
                     "canu correct failed to correct any reads. Advancing with uncorrected reads"
                 )
-                corrected_fastqs = plasmidfastqs
+                corrected_fastqs = entropy_filtered_fastq
 
             unicycler_dir: Path = Path(outdir) / "unicycler_output"
             run_unicycler_long(threads, logdir, corrected_fastqs, unicycler_dir)

src/plassembler/utils/run_canu.py

@@ -151,6 +151,28 @@ def filter_entropy(canu_fasta, outdir):
 
     return output_filename
 
+def filter_entropy_fastqs(fastq: Path, output_filename: Path) -> None:
+    """Filter FASTQ records based on entropy and write the filtered records to a new FASTQ file.
+
+    :param canu_fastq: Input FASTQ file containing long read sequences.
+    :param outdir: Output directory for the filtered FASTQ file.
+    :return: Path to the filtered FASTQ file.
+    """
+
+    filtered_records = []
+
+    for record in SeqIO.parse(fastq, "fastq"):
+        entropy = shannon_entropy_5mers(str(record.seq))
+        if entropy > 5:
+            # Reject low entropy sequences - adjust the threshold as needed.
+            filtered_records.append(record)
+
+    # Write the filtered records to a new FASTQ file.
+    with open(output_filename, "w") as output_handle:
+        SeqIO.write(filtered_records, output_handle, "fastq")
+
+
+
 
 """
 trim contigs

tests/test_end_to_end.py

@@ -153,17 +153,16 @@ def test_plassembler_flye_assembly_info(self):
 
     # flye_dir
     def test_plassembler_flye_dir(self):
-        with self.assertRaises(RuntimeError):
-            """test plassembler run case 4. With flye directory. Should error out (Saves time)."""
-            longreads: Path = f"{end_to_end}/abaumanii_plasmid.fastq.gz"
-            s1: Path = f"{end_to_end}/abaumanii_reads_R1.fastq.gz"
-            s2: Path = f"{end_to_end}/abaumanii_reads_R2.fastq.gz"
-            flye_dir: Path = f"{end_to_end}/abaumanii_plasmid_flye_output"
-            chromosome = 1000000
-            outdir: Path = f"{end_to_end}/test_out"
-            cmd = f"plassembler run -l {longreads} -c {chromosome} -1 {s1} -2 {s2} -d {plassembler_db_dir} -o {outdir}  -t 8 --flye_info {flye_info} -f"
-            exec_command(cmd)
-            remove_directory(outdir)
+        """test plassembler run case 4. With flye directory.."""
+        longreads: Path = f"{end_to_end}/abaumanii_plasmid.fastq.gz"
+        s1: Path = f"{end_to_end}/abaumanii_reads_R1.fastq.gz"
+        s2: Path = f"{end_to_end}/abaumanii_reads_R2.fastq.gz"
+        flye_dir: Path = f"{end_to_end}/abaumanii_plasmid_flye_output"
+        chromosome = 1000000
+        outdir: Path = f"{end_to_end}/test_out"
+        cmd = f"plassembler run -l {longreads} -c {chromosome} -1 {s1} -2 {s2} -d {plassembler_db_dir} -o {outdir}  -t 8 --flye_dir {flye_dir} -f"
+        exec_command(cmd)
+        remove_directory(outdir)
 
     def test_plassembler_flye_assembly_info_missing(self):
         with self.assertRaises(RuntimeError):

tests/test_plass_class.py

@@ -155,7 +155,7 @@ def test_combine_tsv(self):
         plasmid_fasta = Path(f"{assembly_depth_dir}/plasmids.fasta")
         assembly.get_depth(logdir, pacbio_model, threads)
         assembly.process_mash_tsv(plassembler_db_dir, plasmid_fasta)
-        assembly.combine_depth_mash_tsvs(prefix)
+        assembly.combine_depth_mash_tsvs(prefix, False)
         remove_file(Path(f"{assembly_depth_dir}/combined_long.sam"))
         remove_file(Path(f"{assembly_depth_dir}/combined_short.bam"))
         remove_file(Path(f"{assembly_depth_dir}/combined_sorted_long.bam"))

tests/test_plassembler.py

@@ -125,16 +125,18 @@ def test_fasta_input(self):
     # assembled multifasta chrom
     def test_validate_fastas_assembled_mode_multiFASTA(self):
         with self.assertRaises(SystemExit):
-            input_plasmids = os.path.join(val_data, "test.fasta")
-            input_chromosome = os.path.join(val_data, "test_multi.fasta")
-            validate_fastas_assembled_mode(input_chromosome, input_plasmids)
+            input_plasmids: Path = Path(val_data) / "test.fasta"
+            input_chromosome: Path = Path(val_data) / "test_multi.fasta"
+            no_copy_numbers = False
+            validate_fastas_assembled_mode(input_chromosome, input_plasmids, no_copy_numbers)
 
     # assembled single chrom works fine
     def test_validate_fastas_assembled_mode_single(self):
-        input_plasmids = os.path.join(val_data, "test.fasta")
-        input_chromosome = os.path.join(val_data, "test.fasta")
+        input_chromosome: Path = Path(val_data) / "test.fasta"
+        input_plasmids: Path = Path(val_data) / "test.fasta"
+        no_copy_numbers = False
         tmp = 1
-        validate_fastas_assembled_mode(input_chromosome, input_plasmids)
+        validate_fastas_assembled_mode(input_chromosome, input_plasmids, no_copy_numbers)
         self.assertEqual(tmp, 1)
 
     # no gzip