diff options
| -rwxr-xr-x | scripts/from_genbank_to_fasta_and_yaml.py | 31 |
1 files changed, 24 insertions, 7 deletions
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py index 7c64b98..060c314 100755 --- a/scripts/from_genbank_to_fasta_and_yaml.py +++ b/scripts/from_genbank_to_fasta_and_yaml.py @@ -96,13 +96,21 @@ for path_dict_xxx_csv in [os.path.join(dir_dict_ontology_standardization, name_x term_to_uri_dict[term] = uri species_to_taxid_dict = { - 'Homo sapiens': 'http://purl.obolibrary.org/obo/NCBITaxon_9606' + 'Homo sapiens': 'http://purl.obolibrary.org/obo/NCBITaxon_9606', + 'Mustela lutreola': 'http://purl.obolibrary.org/obo/NCBITaxon_9666', + 'Manis javanica': 'http://purl.obolibrary.org/obo/NCBITaxon_9974', + 'Felis catus': 'http://purl.obolibrary.org/obo/NCBITaxon_9685', + 'Panthera tigris jacksoni': 'http://purl.obolibrary.org/obo/NCBITaxon_419130', + 'Canis lupus familiaris': 'http://purl.obolibrary.org/obo/NCBITaxon_9615' } if not os.path.exists(dir_fasta_and_yaml): os.makedirs(dir_fasta_and_yaml) +min_len_to_count = 27500 +num_seq_with_len_ge_X_bp = 0 + missing_value_list = [] for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) for name_metadata_xxx_xml in os.listdir(dir_metadata) if name_metadata_xxx_xml.endswith('.xml')]: @@ -117,7 +125,7 @@ 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) + #print(path_metadata_xxx_xml, accession_version) # A general default-empty yaml could be read from the definitive one info_for_yaml_dict = { @@ -204,6 +212,9 @@ 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]] + elif GBQualifier_value_text_list[0] and ('MT215193' in accession_version or 'MT270814' in accession_version): + # Information checked manually from NCBI Virus + info_for_yaml_dict['host']['host_species'] = species_to_taxid_dict['Canis lupus familiaris'] else: missing_value_list.append('\t'.join([accession_version, 'host_species', GBQualifier_value_text_list[0]])) @@ -220,7 +231,6 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) # - Homo sapiens; male; age 29 --> ['Homo sapiens', 'male', 'age 29'] # - Homo sapiens; symptomatic --> ['Homo sapiens', 'symptomatic'] if len(GBQualifier_value_text_list) > 1: - print(GBQualifier_value_text_list) host_sex = '' if 'female' in GBQualifier_value_text_list[1]: host_sex = 'female' @@ -250,8 +260,6 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) 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 @@ -261,12 +269,15 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) if GBQualifier_value_text.upper() in term_to_uri_dict: GBQualifier_value_text = GBQualifier_value_text.upper() # For example, in case of 'usa: wa' + # Little cleaning + GBQualifier_value_text = GBQualifier_value_text.strip("/'") + if GBQualifier_value_text in term_to_uri_dict: info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict[GBQualifier_value_text]] else: - if GBQualifier_value_text in ['NP/OP swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'np/np swab', 'np/op']: + if GBQualifier_value_text.lower() in ['np/op', 'np/op swab', 'np/np swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab']: info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['oropharyngeal swab']] - elif GBQualifier_value_text in ['nasopharyngeal swab/throat swab', 'nasopharyngeal/throat swab']: + elif GBQualifier_value_text in ['nasopharyngeal swab/throat swab', 'nasopharyngeal/throat swab', 'nasopharyngeal swab and throat swab', 'nasal swab and throat swab']: info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['throat swab']] elif GBQualifier_value_text in ['nasopharyngeal aspirate/throat swab']: info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal aspirate'], term_to_uri_dict['throat swab']] @@ -332,6 +343,12 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) json.dump(info_for_yaml_dict, fw, indent=2) + if(len(GBSeq_sequence.text) >= min_len_to_count): + num_seq_with_len_ge_X_bp += 1 + + if len(missing_value_list) > 0: with open('missing_terms.tsv', 'w') as fw: fw.write('\n'.join(missing_value_list)) + +print('Num. sequences with length >= {} bp: {}'.format(min_len_to_count, num_seq_with_len_ge_X_bp)) |