diff options
Diffstat (limited to 'scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py')
| -rwxr-xr-x | scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py | 10 |
1 files changed, 6 insertions, 4 deletions
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 d76f56b..4bb4964 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 @@ -4,6 +4,8 @@ import argparse parser = argparse.ArgumentParser() parser.add_argument('--skip-request', action='store_true', help='skip metadata and sequence request', required=False) parser.add_argument('--only-missing-id', action='store_true', help='download only missing id', required=False) +parser.add_argument('--dict-ontology', type=str, help='where is the ontology', + default='../dict_ontology_standardization/',required=False) args = parser.parse_args() from Bio import Entrez @@ -22,7 +24,7 @@ num_ids_for_request = 100 dir_metadata = 'metadata_from_nuccore' dir_fasta_and_yaml = 'fasta_and_yaml' -dir_dict_ontology_standardization = '../dict_ontology_standardization/' +dir_dict_ontology_standardization = args.dict_ontology today_date = date.today().strftime("%Y.%m.%d") path_ncbi_virus_accession = 'sequences.{}.acc'.format(today_date) @@ -126,7 +128,7 @@ for path_dict_xxx_csv in [os.path.join(dir_dict_ontology_standardization, name_x if term in term_to_uri_dict: print('Warning: in the dictionaries there are more entries for the same term ({}).'.format(term)) continue - + term_to_uri_dict[term] = uri if not os.path.exists(dir_fasta_and_yaml): @@ -274,7 +276,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) if host_sex in ['male', 'female']: info_for_yaml_dict['host']['host_sex'] = "http://purl.obolibrary.org/obo/PATO_0000384" if host_sex == 'male' else "http://purl.obolibrary.org/obo/PATO_0000383" elif GBQualifier_value_text_list[1] in term_to_uri_dict: - info_for_yaml_dict['host']['host_health_status'] = term_to_uri_dict[GBQualifier_value_text_list[1]] + info_for_yaml_dict['host']['host_health_status'] = term_to_uri_dict[GBQualifier_value_text_list[1]] else: missing_value_list.append('\t'.join([accession_version, 'host_sex or host_health_status', GBQualifier_value_text_list[1]])) @@ -391,5 +393,5 @@ if len(accession_with_errors_list) > 0: print('Written the accession with errors in {}'.format(path_accession_with_errors_tsv)) with open(path_accession_with_errors_tsv, 'w') as fw: fw.write('\n'.join(accession_with_errors_list)) - + print('Num. new sequences with length >= {} bp: {}'.format(min_len_to_count, num_seq_with_len_ge_X_bp)) |