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):
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 __init__(self, *args, **kwargs):
super(GnomADTask, self).__init__(*args, **kwargs)
self.gnomAD_file_dir = self.cfg.file_parent_dir + "/gnomAD"
self.gnomAD_static_file = "gnomAD.concatted.clean.tsv"
pipeline_utils.create_path_if_nonexistent(self.gnomAD_file_dir)
def __init__(self, *args, **kwargs):
super(ESPTask, self).__init__(*args, **kwargs)
self.esp_file_dir = self.cfg.file_parent_dir + "/ESP"
self.esp_tar_file_name = esp_data_url.split('/')[-1]
pipeline_utils.create_path_if_nonexistent(self.esp_file_dir)
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 __init__(self, *args, **kwargs):
super(ESPTask, self).__init__(*args, **kwargs)
self.esp_file_dir = self.cfg.file_parent_dir + "/ESP"
self.esp_tar_file_name = esp_data_url.split('/')[-1]
pipeline_utils.create_path_if_nonexistent(self.esp_file_dir)
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 __init__(self, *args, **kwargs):
super(GnomADTask, self).__init__(*args, **kwargs)
self.gnomAD_file_dir = self.cfg.file_parent_dir + "/gnomAD"
self.gnomAD_download_file_name = "gnomAD.tsv"
pipeline_utils.create_path_if_nonexistent(self.gnomAD_file_dir)