diff options
| -rwxr-xr-x | scripts/from_genbank_to_fasta_and_yaml.py | 62 |
1 files changed, 52 insertions, 10 deletions
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py index 0c49c65..7c64b98 100755 --- a/scripts/from_genbank_to_fasta_and_yaml.py +++ b/scripts/from_genbank_to_fasta_and_yaml.py @@ -20,6 +20,13 @@ dir_dict_ontology_standardization = 'dict_ontology_standardization/' today_date = date.today().strftime("%Y.%m.%d") path_ncbi_virus_accession = 'sequences.{}.acc'.format(today_date) +def is_integer(string_to_check): + try: + int(string_to_check) + return True + except ValueError: + return False + def chunks(lst, n): for i in range(0, len(lst), n): yield lst[i:i + n] @@ -72,6 +79,7 @@ if not os.path.exists(dir_metadata): Entrez.efetch(db='nuccore', id=id_x_list, retmode='xml').read() ) + term_to_uri_dict = {} for path_dict_xxx_csv in [os.path.join(dir_dict_ontology_standardization, name_xxx_csv) for name_xxx_csv in os.listdir(dir_dict_ontology_standardization) if name_xxx_csv.endswith('.csv')]: @@ -109,6 +117,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) print(accession_version, ' - sequence not found') continue + print(path_metadata_xxx_xml, accession_version) # A general default-empty yaml could be read from the definitive one info_for_yaml_dict = { @@ -195,21 +204,54 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) if GBQualifier_value_text_list[0] in species_to_taxid_dict: info_for_yaml_dict['host']['host_species'] = species_to_taxid_dict[GBQualifier_value_text_list[0]] - + else: + missing_value_list.append('\t'.join([accession_version, 'host_species', GBQualifier_value_text_list[0]])) + + # Possible cases: + # - Homo sapiens --> ['Homo sapiens'] + # - Homo sapiens; female --> ['Homo sapiens', 'female'] + # - Homo sapiens; female 63 --> ['Homo sapiens', 'female 63'] + # - Homo sapiens; female; age 40 --> ['Homo sapiens', 'female', 'age 40'] + # - Homo sapiens; gender: F; age: 61 --> ['Homo sapiens', 'gender: F', 'age: 61'] + # - Homo sapiens; gender: M; age: 68 --> ['Homo sapiens', 'gender: M', 'age: 68'] + # - Homo sapiens; hospitalized patient --> ['Homo sapiens', 'hospitalized patient'] + # - Homo sapiens; male --> ['Homo sapiens', 'male'] + # - Homo sapiens; male; 63 --> ['Homo sapiens', 'male', '63'] + # - Homo sapiens; male; age 29 --> ['Homo sapiens', 'male', 'age 29'] + # - Homo sapiens; symptomatic --> ['Homo sapiens', 'symptomatic'] if len(GBQualifier_value_text_list) > 1: - if GBQualifier_value_text_list[1] in ['male', 'female']: - if GBQualifier_value_text_list[1]=='male': - info_for_yaml_dict['host']['host_sex'] = "http://purl.obolibrary.org/obo/PATO_0000384" - elif GBQualifier_value_text_list[1]=='female': - info_for_yaml_dict['host']['host_sex'] = "http://purl.obolibrary.org/obo/PATO_0000383" + print(GBQualifier_value_text_list) + host_sex = '' + if 'female' in GBQualifier_value_text_list[1]: + host_sex = 'female' + elif 'male' in GBQualifier_value_text_list[1]: + host_sex = 'male' + elif 'gender' in GBQualifier_value_text_list[1]: + host_sex_one_lecter = GBQualifier_value_text_list[1].split(':')[-1].strip() + if host_sex_one_lecter in ['F', 'M']: + host_sex = 'female' if host_sex_one_lecter == 'F' else 'male' + + 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, GBQualifier_name_text, GBQualifier_value_text_list[1]])) + missing_value_list.append('\t'.join([accession_version, 'host_sex or host_health_status', GBQualifier_value_text_list[1]])) + + # Host age + host_age = -1 + if len(GBQualifier_value_text_list[1].split(' ')) > 1 and is_integer(GBQualifier_value_text_list[1].split(' ')[-1]): + host_age = int(GBQualifier_value_text_list[1].split(' ')[-1]) + elif len(GBQualifier_value_text_list) > 2 and is_integer(GBQualifier_value_text_list[2].split(' ')[-1]): + host_age = int(GBQualifier_value_text_list[2].split(' ')[-1]) - if 'age' in GBQualifier_value_text: - info_for_yaml_dict['host']['host_age'] = int(GBQualifier_value_text_list[2].split('age ')[1]) + if host_age > -1: + info_for_yaml_dict['host']['host_age'] = host_age info_for_yaml_dict['host']['host_age_unit'] = 'http://purl.obolibrary.org/obo/UO_0000036' + elif len(GBQualifier_value_text_list) > 2: + missing_value_list.append('\t'.join([accession_version, 'host_age', GBQualifier_value_text_list[2]])) + + print('host_sex {} - host_age {}'.format(host_sex, host_age), '<--', GBQualifier_value_text_list) elif GBQualifier_name_text == 'collected_by': if any([x in GBQualifier_value_text.lower() for x in ['institute', 'hospital', 'city', 'center']]): info_for_yaml_dict['sample']['collecting_institution'] = GBQualifier_value_text |