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)