import os
import yaml
from pathlib import Path
[docs]def get_chrom(panelfile):
"""
input: a panel bedfile
output: list of chromosomes in the bedfile
"""
lines = [line.rstrip('\n') for line in open(panelfile, 'r')]
chrom = list(set([s.split('\t')[0] for s in lines]))
return chrom
[docs]def get_vcf(config, var_caller, sample):
"""
input: BALSAMIC config file
output: retrieve list of vcf files
"""
vcf = []
for v in var_caller:
for s in sample:
vcf.append(config["vcf"][v]["type"] + "." +
config["vcf"][v]["mutation"] + "." + s + "." + v)
return vcf
[docs]def get_sample_type(sample, bio_type):
"""
input: sample dictionary from BALSAMIC's config file
output: list of sample type id
"""
type_id = []
for sample_id in sample:
if sample[sample_id]["type"] == bio_type:
type_id.append(sample_id)
return type_id
[docs]def get_result_dir(config):
"""
input: sample config file from BALSAMIC
output: string of result directory path
"""
return config['analysis']['result']
[docs]def get_conda_env(yaml_file, pkg):
"""
input: balsamic_env
output: string of conda env where packge is in
"""
yaml_in = yaml.safe_load(open(yaml_file))
conda_env_found = None
for conda_env, pkgs in yaml_in.items():
if pkg in pkgs:
conda_env_found = conda_env
break
if conda_env_found is not None:
return conda_env_found
else:
raise KeyError(f'Installed package {pkg} was not found in {yaml_file}')
[docs]def get_picard_mrkdup(config):
"""
input: sample config file output from BALSAMIC
output: mrkdup or rmdup strings
"""
picard_str = "mrkdup"
if "picard_rmdup" in config["QC"]:
if config["QC"]["picard_rmdup"] == True:
picard_str = "rmdup"
return picard_str
[docs]def get_script_path(script_name: str):
"""
Retrieves script path where name is matching {{script_name}}.
"""
p = Path(__file__).parents[1]
script_path = str(Path(p, 'assets/scripts', script_name))
return script_path
[docs]def get_threads(cluster_config, rule_name='__default__'):
"""
To retrieve threads from cluster config or return default value of 8
"""
return cluster_config[rule_name]['n'] if rule_name in cluster_config else 8