diff options
| -rw-r--r-- | scripts/create_sra_metadata/create_sra_metadata.py | 29 | ||||
| -rwxr-xr-x | scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py | 3 |
2 files changed, 28 insertions, 4 deletions
diff --git a/scripts/create_sra_metadata/create_sra_metadata.py b/scripts/create_sra_metadata/create_sra_metadata.py index 09cc51b..7e0fc83 100644 --- a/scripts/create_sra_metadata/create_sra_metadata.py +++ b/scripts/create_sra_metadata/create_sra_metadata.py @@ -3,6 +3,7 @@ import argparse parser = argparse.ArgumentParser() parser.add_argument('--ids-to-ignore', type=str, help='file with ids to ignore in all steps, 1 id per line', required=False) +parser.add_argument('--ids-to-consider', type=str, help='file with ids to consider in all steps, 1 id per line', required=False) parser.add_argument('--dict-ontology', type=str, help='where is the ontology', default='../dict_ontology_standardization/', required=False) @@ -45,7 +46,22 @@ if args.ids_to_ignore: with open(args.ids_to_ignore) as f: accession_to_ignore_set.update(set([x.split('.')[0] for x in f.read().strip('\n').split('\n')])) - print('There are {} accessions to ignore.'.format(len(accession_to_ignore_set))) + + print('There are {} accessions to ignore.'.format(len(accession_to_ignore_set))) + + +accession_to_consider_set = set() + +if args.ids_to_consider: + if not os.path.exists(args.ids_to_consider): + print("\tThe '{}' file doesn't exist.".format(args.ids_to_consider)) + sys.exit(-1) + + with open(args.ids_to_consider) as f: + accession_to_consider_set.update(set([x.split('.')[0] for x in f.read().strip('\n').split('\n')])) + + if len(accession_to_consider_set) > 0: + print('There are {} accessions to consider.'.format(len(accession_to_consider_set))) term_to_uri_dict = {} @@ -103,9 +119,16 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): RUN_SET = EXPERIMENT_PACKAGE.find('RUN_SET') RUN = RUN_SET.find('RUN') accession = RUN.attrib['accession'] + run_accession_set.add(accession) #print(accession) + if accession in accession_to_ignore_set: + continue + + if len(accession_to_consider_set) > 0 and accession not in accession_to_consider_set: + continue + info_for_yaml_dict['sample']['sample_id'] = accession #SRAFiles = RUN.find('SRAFiles') @@ -305,8 +328,8 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): if accession not in not_created_accession_dict: num_yaml_created += 1 - with open(os.path.join(dir_yaml, '{}.yaml'.format(accession)), 'w') as fw: - json.dump(info_for_yaml_dict, fw, indent=2) + #with open(os.path.join(dir_yaml, '{}.yaml'.format(accession)), 'w') as fw: + # json.dump(info_for_yaml_dict, fw, indent=2) if len(missing_value_list) > 0: path_missing_terms_tsv = 'missing_terms.sra.tsv' diff --git a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py index 7251819..52aee4e 100755 --- a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py +++ b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py @@ -58,7 +58,8 @@ if args.ids_to_ignore: with open(args.ids_to_ignore) as f: accession_to_ignore_set.update(set([x.split('.')[0] for x in f.read().strip('\n').split('\n')])) - print('There are {} accessions to ignore.'.format(len(accession_to_ignore_set))) + + print('There are {} accessions to ignore.'.format(len(accession_to_ignore_set))) accession_already_downloaded_set = set() |