def main():
parser = argparse.ArgumentParser(
description='Generate custom assembly report for a given assembly',
add_help=False)
parser.add_argument(
"-a",
"--assembly-accession",
help=
"Assembly for which the process has to be run, e.g. GCA_000002315.3",
required=True)
parser.add_argument("-f",
"--fasta-file",
help="Path to the fasta file containing the assembly",
required=True)
parser.add_argument(
"-r",
"--report-file",
help="Path to the assembly report file containing the assembly",
required=True)
parser.add_argument('--help',
action='help',
help='Show this help message and exit')
args = parser.parse_args()
load_config()
logging_config.add_stdout_handler()
assembly = CustomAssemblyFromDatabase(args.assembly_accession,
args.fasta_file, args.report_file)
assembly.generate_assembly_report()
assembly.generate_fasta()
def main():
argparse = ArgumentParser(
description=
'Run entire variant remapping pipeline for a given assembly and taxonomy.'
)
argparse.add_argument('--assembly', help='Assembly to be process')
argparse.add_argument('--taxonomy_id', help='Taxonomy id to be process')
argparse.add_argument('--list_jobs',
help='Display the list of jobs to be run.',
action='store_true',
default=False)
argparse.add_argument(
'--resume',
help='If a process has been run already this will resume it.',
action='store_true',
default=False)
args = argparse.parse_args()
load_config()
if args.list_jobs:
RemappingJob().list_assemblies_to_process()
elif args.assembly and args.taxonomy_id:
logging_config.add_stdout_handler()
RemappingJob().process_one_assembly(args.assembly, args.taxonomy_id,
args.resume)
else:
raise ArgumentError(
'One of (--assembly and --taxonomy_id) or --list_jobs options is required'
)
def main():
argparse = ArgumentParser(description='Run remediation for one assembly')
argparse.add_argument('--assembly', help='Source assembly to remediate')
argparse.add_argument('--resume', action='store_true', default=False)
args = argparse.parse_args()
load_config()
process_one_assembly(args.assembly, args.resume)
def setUp(self) -> None:
config_file = os.path.join(self.resources_folder, 'remapping_config.yml')
load_config(config_file)
assembly_accession = 'GCA_000003055.3'
assembly_report_path = os.path.join(self.resources_folder, 'GCA_000003055.3_assembly_report.txt')
assembly_fasta_path = os.path.join(self.resources_folder, 'GCA_000003055.3.fa')
self.assembly = CustomAssemblyFromDatabase(assembly_accession, assembly_fasta_path, assembly_report_path)
self.patch_get_results = patch('get_custom_assembly.get_all_results_for_query', return_value=[('AY526085.1', 'RefSeq')])
self.patch_get_conn = patch('get_custom_assembly.get_metadata_connection_handle')
def setUp(self) -> None:
config_file = os.path.join(self.resources_folder, 'remapping_config.yml')
load_config(config_file)
assembly_accession = 'GCA_000003055.3'
assembly_report_path = os.path.join(self.resources_folder, 'GCA_000003055.3_assembly_report.txt')
assembly_fasta_path = os.path.join(self.resources_folder, 'GCA_000003055.3.fa')
self.assembly = CustomAssembly(assembly_accession, assembly_fasta_path, assembly_report_path)
self.patch_required_contigs = patch.object(
CustomAssembly, 'required_contigs',
new_callable=PropertyMock(return_value=[{'genbank': 'AY526085.1', 'refseq': 'RefSeq'}])
)
self.patch_required_contigs_none = patch.object(
CustomAssembly, 'required_contigs',
new_callable=PropertyMock(return_value=[])
)
self.current_dir = os.getcwd()
os.chdir(os.path.dirname(os.path.dirname(__file__)))