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Merge branch 'master' into feat-update-consensus-peaks
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@alsmith151
alsmith151 committed Feb 9, 2024
2 parents b7601f5 + 07f8420 commit 9c754a0
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Showing 5 changed files with 178 additions and 323 deletions.
211 changes: 143 additions & 68 deletions seqnado/config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,33 +6,40 @@
package_dir = os.path.dirname(os.path.abspath(__file__))
template_dir = os.path.join(package_dir, "workflow/config")


# Helper Functions
def get_user_input(prompt, default=None, is_boolean=False, choices=None):
while True:
user_input = input(f"{prompt} [{'/'.join(choices) if choices else default}]: ") or default
user_input = (
input(f"{prompt} [{'/'.join(choices) if choices else default}]: ")
or default
)
if is_boolean:
return user_input.lower() == 'yes'
return user_input.lower() == "yes"
if choices and user_input not in choices:
print(f"Invalid choice. Please choose from {', '.join(choices)}.")
continue
return user_input


def setup_configuration(assay, genome, template_data):
username = os.getenv('USER', 'unknown_user')
today = datetime.datetime.now().strftime('%Y-%m-%d')
project_name = get_user_input("What is your project name?", default=f"{username}_project")
username = os.getenv("USER", "unknown_user")
today = datetime.datetime.now().strftime("%Y-%m-%d")
project_name = get_user_input(
"What is your project name?", default=f"{username}_project"
)
project_name = project_name.replace(" ", "_")

common_config = {
'username': username,
'project_date': today,
'project_name': project_name,
'genome': genome
"username": username,
"project_date": today,
"project_name": project_name,
"genome": genome,
}

template_data.update(common_config)

with open(os.path.join(template_dir, 'preset_genomes.json'), 'r') as f:
with open(os.path.join(template_dir, "preset_genomes.json"), "r") as f:
genome_values = json.load(f)

genome_dict = {}
Expand All @@ -41,72 +48,135 @@ def setup_configuration(assay, genome, template_data):
genome = get_user_input("What is your genome name?", default="other")
genome_dict = {
genome: {
"indices": get_user_input("Path to Bowtie2 genome indices:") if assay in ["chip", "atac"] else get_user_input("Path to STAR v2.7.10b genome indices:"),
"indices": (
get_user_input("Path to Bowtie2 genome indices:")
if assay in ["chip", "atac"]
else get_user_input("Path to STAR v2.7.10b genome indices:")
),
"chromosome_sizes": get_user_input("Path to chromosome sizes file:"),
"gtf": get_user_input("Path to GTF file:"),
"blacklist": get_user_input("Path to blacklist bed file:")
"blacklist": get_user_input("Path to blacklist bed file:"),
}
}
else:
if genome in genome_values:
genome_dict[genome] = {
"indices": genome_values[genome].get('bt2_indices' if assay in ["chip", "atac"] else 'star_indices', ''),
"chromosome_sizes": genome_values[genome].get('chromosome_sizes', ''),
"gtf": genome_values[genome].get('gtf', ''),
"blacklist": genome_values[genome].get('blacklist', '')
"indices": genome_values[genome].get(
"bt2_indices" if assay in ["chip", "atac"] else "star_indices", ""
),
"chromosome_sizes": genome_values[genome].get("chromosome_sizes", ""),
"gtf": genome_values[genome].get("gtf", ""),
"blacklist": genome_values[genome].get("blacklist", ""),
}


genome_config = {
'genome': genome,
'indices': genome_dict[genome]['indices'],
'chromosome_sizes': genome_dict[genome]['chromosome_sizes'],
'gtf': genome_dict[genome]['gtf'],
"genome": genome,
"indices": genome_dict[genome]["indices"],
"chromosome_sizes": genome_dict[genome]["chromosome_sizes"],
"gtf": genome_dict[genome]["gtf"],
}
template_data.update(genome_config)


template_data['remove_blacklist'] = get_user_input("Do you want to remove blacklist regions? (yes/no)", default="yes", is_boolean=True)
if template_data['remove_blacklist']:
template_data['blacklist'] = genome_dict[genome]['blacklist']

template_data['remove_pcr_duplicates'] = get_user_input("Remove PCR duplicates? (yes/no)", default= "yes" if assay in ["chip", "atac"] else "no", is_boolean=True)
if template_data['remove_pcr_duplicates']:
template_data['remove_pcr_duplicates_method'] = get_user_input("Remove PCR duplicates method:", default="picard", choices=["picard"])
template_data["remove_blacklist"] = get_user_input(
"Do you want to remove blacklist regions? (yes/no)",
default="yes",
is_boolean=True,
)
if template_data["remove_blacklist"]:
template_data["blacklist"] = genome_dict[genome]["blacklist"]

template_data["remove_pcr_duplicates"] = get_user_input(
"Remove PCR duplicates? (yes/no)",
default="yes" if assay in ["chip", "atac"] else "no",
is_boolean=True,
)
if template_data["remove_pcr_duplicates"]:
template_data["remove_pcr_duplicates_method"] = get_user_input(
"Remove PCR duplicates method:", default="picard", choices=["picard"]
)

else:
template_data['remove_pcr_duplicates_method'] = "False"
template_data["remove_pcr_duplicates_method"] = "False"

if assay == "atac":
template_data['shift_atac_reads'] = get_user_input("Shift ATAC-seq reads? (yes/no)", default="yes", is_boolean=True) if assay == "atac" else "False"
template_data["shift_atac_reads"] = (
get_user_input(
"Shift ATAC-seq reads? (yes/no)", default="yes", is_boolean=True
)
if assay == "atac"
else "False"
)

if assay == "chip":
template_data['spikein'] = get_user_input("Do you have spikein? (yes/no)", default="no", is_boolean=True)
if template_data['spikein']:
template_data['normalisation_method'] = get_user_input("Normalisation method:", default="orlando", choices=["orlando", "with_input"])
template_data['reference_genome'] = get_user_input("Reference genome:", default="hg38")
template_data['spikein_genome'] = get_user_input("Spikein genome:", default="dm6")
template_data['fastq_screen_config'] = get_user_input("Path to fastqscreen config:", default="/ceph/project/milne_group/shared/seqnado_reference/fastqscreen_reference/fastq_screen.conf")

template_data['make_bigwigs'] = get_user_input("Do you want to make bigwigs? (yes/no)", default="no", is_boolean=True)
if template_data['make_bigwigs']:
template_data['pileup_method'] = get_user_input("Pileup method:", default="deeptools", choices=["deeptools", "homer"])
template_data['make_heatmaps'] = get_user_input("Do you want to make heatmaps? (yes/no)", default="no", is_boolean=True)

if assay in ["chip", "atac"]:
template_data['call_peaks'] = get_user_input("Do you want to call peaks? (yes/no)", default="no", is_boolean=True)
if template_data['call_peaks']:
template_data['peak_calling_method'] = get_user_input("Peak caller:", default="lanceotron", choices=["lanceotron", "macs", "homer"])

template_data['run_deseq2'] = get_user_input("Run DESeq2? (yes/no)", default="no", is_boolean=True) if assay == "rna" else "False"
template_data["spikein"] = get_user_input(
"Do you have spikein? (yes/no)", default="no", is_boolean=True
)
if template_data["spikein"]:
template_data["normalisation_method"] = get_user_input(
"Normalisation method:",
default="orlando",
choices=["orlando", "with_input"],
)
template_data["reference_genome"] = get_user_input(
"Reference genome:", default="hg38"
)
template_data["spikein_genome"] = get_user_input(
"Spikein genome:", default="dm6"
)
template_data["fastq_screen_config"] = get_user_input(
"Path to fastqscreen config:",
default="/ceph/project/milne_group/shared/seqnado_reference/fastqscreen_reference/fastq_screen.conf",
)

template_data["make_bigwigs"] = get_user_input(
"Do you want to make bigwigs? (yes/no)", default="no", is_boolean=True
)
if template_data["make_bigwigs"]:
template_data["pileup_method"] = get_user_input(
"Pileup method:", default="deeptools", choices=["deeptools", "homer"]
)
template_data["make_heatmaps"] = get_user_input(
"Do you want to make heatmaps? (yes/no)", default="no", is_boolean=True
)

template_data['make_ucsc_hub'] = get_user_input("Do you want to make a UCSC hub? (yes/no)", default="no", is_boolean=True)

template_data['UCSC_hub_directory'] = get_user_input("UCSC hub directory:", default="/path/to/ucsc_hub/") if template_data['make_ucsc_hub'] else "."
template_data['email'] = get_user_input("What is your email address?", default=f"{username}@example.com") if template_data['make_ucsc_hub'] else f"{username}@example.com"
template_data['color_by'] = get_user_input("Color by (for UCSC hub):", default="samplename") if template_data['make_ucsc_hub'] else "samplename"

template_data['options'] = TOOL_OPTIONS_RNA if assay == "rna" else TOOL_OPTIONS
if assay in ["chip", "atac"]:
template_data["call_peaks"] = get_user_input(
"Do you want to call peaks? (yes/no)", default="no", is_boolean=True
)
if template_data["call_peaks"]:
template_data["peak_calling_method"] = get_user_input(
"Peak caller:",
default="lanceotron",
choices=["lanceotron", "macs", "homer"],
)

template_data["run_deseq2"] = (
get_user_input("Run DESeq2? (yes/no)", default="no", is_boolean=True)
if assay == "rna"
else "False"
)

template_data["make_ucsc_hub"] = get_user_input(
"Do you want to make a UCSC hub? (yes/no)", default="no", is_boolean=True
)

template_data["UCSC_hub_directory"] = (
get_user_input("UCSC hub directory:", default="/path/to/ucsc_hub/")
if template_data["make_ucsc_hub"]
else "."
)
template_data["email"] = (
get_user_input("What is your email address?", default=f"{username}@example.com")
if template_data["make_ucsc_hub"]
else f"{username}@example.com"
)
template_data["color_by"] = (
get_user_input("Color by (for UCSC hub):", default="samplename")
if template_data["make_ucsc_hub"]
else "samplename"
)

template_data["options"] = TOOL_OPTIONS_RNA if assay == "rna" else TOOL_OPTIONS


# Tool Specific Options
Expand Down Expand Up @@ -178,35 +248,40 @@ def setup_configuration(assay, genome, template_data):
colormap: RdYlBu_r
"""


def create_config(assay, genome, rerun):
env = Environment(loader=FileSystemLoader(template_dir), auto_reload=False)

template = env.get_template("config.yaml.jinja")
template = env.get_template("config.yaml.jinja")
template_deseq2 = env.get_template("deseq2.qmd.jinja")

# Initialize template data
template_data = {'assay': assay, 'genome': genome}
template_data = {"assay": assay, "genome": genome}

# Setup configuration
setup_configuration(assay, genome, template_data)

# Create directory and render template
if rerun:
dir_name = os.getcwd()
with open(os.path.join(dir_name, f"config_{assay}.yml"), 'w') as file:
with open(os.path.join(dir_name, f"config_{assay}.yml"), "w") as file:
file.write(template.render(template_data))
else:
dir_name = f"{template_data['project_date']}_{template_data['assay']}_{template_data['project_name']}"
os.makedirs(dir_name, exist_ok=True)
fastq_dir = os.path.join(dir_name, "fastq")
os.makedirs(fastq_dir, exist_ok=True)
with open(os.path.join(dir_name, f"config_{assay}.yml"), 'w') as file:

with open(os.path.join(dir_name, f"config_{assay}.yml"), "w") as file:
file.write(template.render(template_data))

# add deseq2 qmd file if rna
if assay == "rna":
with open(os.path.join(dir_name, f"deseq2_{template_data['project_name']}.qmd"), 'w') as file:
with open(
os.path.join(dir_name, f"deseq2_{template_data['project_name']}.qmd"), "w"
) as file:
file.write(template_deseq2.render(template_data))

print(f"Directory '{dir_name}' has been created with the 'config_{assay}.yml' file.")

print(
f"Directory '{dir_name}' has been created with the 'config_{assay}.yml' file."
)
72 changes: 23 additions & 49 deletions seqnado/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -683,71 +683,45 @@ def from_dataframe(cls, df: pd.DataFrame, simplified: bool = True, **kwargs):

return cls(assays=experiments, **kwargs)


def symlink_files_paired(
output_dir: pathlib.Path, assay: Union[AssayNonIP, AssayIP], assay_name: str
):
r1_path_new = pathlib.Path(f"{output_dir}/{assay_name}_1.fastq.gz")
r2_path_new = pathlib.Path(f"{output_dir}/{assay_name}_2.fastq.gz")

if not r1_path_new.exists():
try:
r1_path_new.symlink_to(assay.r1.path.resolve())
except FileExistsError:
logger.warning(f"Symlink for {r1_path_new} already exists.")

if assay.r2 and not r2_path_new.exists():
try:
r2_path_new.symlink_to(assay.r2.path.resolve())
except FileExistsError:
logger.warning(f"Symlink for {r2_path_new} already exists.")


def symlink_files_single(
output_dir: pathlib.Path, assay: Union[AssayNonIP, AssayIP], assay_name: str
):
r1_path_new = pathlib.Path(f"{output_dir}/{assay_name}.fastq.gz")

if not r1_path_new.exists():
def symlink_file(output_dir: pathlib.Path, source_path: pathlib.Path, new_file_name: str):
"""
Create a symlink in the output directory with the new file name.
"""
new_path = output_dir / new_file_name
if not new_path.exists():
try:
r1_path_new.symlink_to(assay.r1.path.resolve())
new_path.symlink_to(source_path.resolve())
except FileExistsError:
logger.warning(f"Symlink for {r1_path_new} already exists.")

logger.warning(f"Symlink for {new_path} already exists.")

def symlink_fastq_files(
design: Union[Design, DesignIP], output_dir: str = "seqnado_output/fastqs/"
) -> None:
def symlink_fastq_files(design: Union[Design, DesignIP], output_dir: str = "seqnado_output/fastqs/") -> None:
"""
Symlink the fastq files to the output directory.
"""
output_dir = pathlib.Path(output_dir)
output_dir.mkdir(parents=True, exist_ok=True)

if isinstance(design, Design):
for assay_name, assay in design.assays.items():
symlink_file(output_dir, assay.r1.path, f"{assay_name}_1.fastq.gz")
if assay.is_paired:
symlink_files_paired(output_dir, assay, assay_name)
else:
symlink_files_single(output_dir, assay, assay_name)
symlink_file(output_dir, assay.r2.path, f"{assay_name}_2.fastq.gz")

elif isinstance(design, DesignIP):
for experiment_name, experiment in design.assays.items():
assay = experiment.ip_files
assay_name = assay.name

if assay.is_paired:
symlink_files_paired(output_dir, assay, assay_name)
else:
symlink_files_single(output_dir, assay, assay_name)
# IP files
ip_assay = experiment.ip_files
symlink_file(output_dir, ip_assay.r1.path, f"{ip_assay.name}_1.fastq.gz")
if ip_assay.is_paired:
symlink_file(output_dir, ip_assay.r2.path, f"{ip_assay.name}_2.fastq.gz")

if experiment.control_files:
assay = experiment.control_files
assay_name = assay.name
if assay.is_paired:
symlink_files_paired(output_dir, assay, assay_name)
else:
symlink_files_single(output_dir, assay, assay_name)
control_assay = experiment.control_files
control_r1_name = control_assay.r1.path.name
symlink_file(output_dir, control_assay.r1.path, control_r1_name)
if control_assay.is_paired:
control_r2_name = control_assay.r2.path.name
symlink_file(output_dir, control_assay.r2.path, control_r2_name)


def define_output_files(
Expand Down
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