def run(self):
brca_resources_dir = self.cfg.resources_dir
artifacts_dir = pipeline_utils.create_path_if_nonexistent(
self.cfg.output_dir + "/release/artifacts")
os.chdir(gnomAD_method_dir)
args = [
"python", "gnomad_to_vcf.py", "-i",
self.input().path, "-o",
self.output().path, "-a", "gnomADAnnotation", "-r",
brca_resources_dir + "/refseq_annotation.hg19.gp", "-g",
brca_resources_dir + "/hg19.fa", "-l",
artifacts_dir + "/gnomAD_error_variants.log", "-s", "gnomAD"
]
logger.info("Running gnomad_to_vcf.py with the following args: %s",
args)
sp = subprocess.Popen(args,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
pipeline_utils.print_subprocess_output_and_error(sp)
pipeline_utils.check_file_for_contents(self.output().path)
def run(self):
with open(self.output().path, 'w') as f:
args = ["vcf-sort", self.input().path]
logger.info("Running vcf-sort with the following args: %s", args)
sp = subprocess.Popen(args, stdout=f, stderr=subprocess.PIPE)
pipeline_utils.print_subprocess_output_and_error(sp)
pipeline_utils.check_file_for_contents(self.output().path)
logger.info("Sorting of concatenated files complete.")
def run(self):
brca_resources_dir = self.cfg.resources_dir
args = ["CrossMap.py", "vcf", brca_resources_dir + "/hg19ToHg38.over.chain.gz",
self.gnomAD_file_dir + "/gnomAD.clean.hg19.vcf", brca_resources_dir + "/hg38.fa",
self.gnomAD_file_dir + "/gnomAD.clean.hg38.vcf"]
logger.info("Running CrossMap.py with the following args: %s", args)
sp = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
pipeline_utils.print_subprocess_output_and_error(sp)
pipeline_utils.check_file_for_contents(self.output().path)
def run(self):
sorted_concatenated_brca_output_file = self.output().path
concatenated_brca_output_file = self.input().path
with open(sorted_concatenated_brca_output_file, 'w') as f:
args = ["vcf-sort", concatenated_brca_output_file]
logger.info("Calling vcf-sort with the following args: %s", args)
sp = subprocess.Popen(args, stdout=f, stderr=subprocess.PIPE)
pipeline_utils.print_subprocess_output_and_error(sp)
pipeline_utils.check_file_for_contents(
sorted_concatenated_brca_output_file)
logger.info("Sorting of concatenated files complete.")
def run(self):
concatenated_brca_output_file = self.output().path
with open(concatenated_brca_output_file, 'w') as f:
# Note: requires correct installation of VCF tools and export PERL5LIB=/path/to/your/vcftools-directory/src/perl/ in path
args = ["vcf-concat"]
args.extend([t.path for t in self.input()])
logger.info("Calling vcf-concat with the following args: %s", args)
sp = subprocess.Popen(args, stdout=f, stderr=subprocess.PIPE)
pipeline_utils.print_subprocess_output_and_error(sp)
pipeline_utils.check_file_for_contents(concatenated_brca_output_file)
logger.info("Concatenation complete.")
def run(self):
concatenated_brca_output_file = self.output().path
with open(concatenated_brca_output_file, 'w') as f:
# Note: requires correct installation of VCF tools and export PERL5LIB=/path/to/your/vcftools-directory/src/perl/ in path
args = ["vcf-concat"]
args.extend([t.path for t in self.input()])
logger.info("Calling vcf-concat with the following args: %s", args)
sp = subprocess.Popen(args, stdout=f, stderr=subprocess.PIPE)
pipeline_utils.print_subprocess_output_and_error(sp)
pipeline_utils.check_file_for_contents(concatenated_brca_output_file)
logger.info("Concatenation complete.")
def run(self):
artifacts_dir = pipeline_utils.create_path_if_nonexistent(
self.cfg.output_dir + "/release/artifacts")
os.chdir(gnomAD_method_dir)
args = [
"python", "download_gnomad_data.py", "-o",
self.output().path, "-l",
artifacts_dir + "/download_gnomAD_data.log"
]
sp = subprocess.Popen(args,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
pipeline_utils.print_subprocess_output_and_error(sp)
pipeline_utils.check_file_for_contents(self.output().path)
def run(self):
os.chdir(gnomAD_method_dir)
args = [
"python", "parse_gnomad_data.py", "-i",
self.input().path, "-o",
self.output().path
]
logger.info("Running parse_gnomad_data.py with the following args: %s",
args)
sp = subprocess.Popen(args,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
pipeline_utils.print_subprocess_output_and_error(sp)
pipeline_utils.check_file_for_contents(self.output().path)
def run(self):
pipeline_utils.create_path_if_nonexistent(
os.path.dirname(self.output().path))
copy(self.req_task.output().path, self.output().path)
pipeline_utils.check_file_for_contents(self.output().path)
def run(self):
pipeline_utils.create_path_if_nonexistent(
os.path.dirname(self.output().path))
copy(self.req_task.output().path, self.output().path)
pipeline_utils.check_file_for_contents(self.output().path)