diff options
Diffstat (limited to 'scripts/from_genbank_to_fasta_and_yaml.py')
| -rwxr-xr-x | scripts/from_genbank_to_fasta_and_yaml.py | 96 |
1 files changed, 61 insertions, 35 deletions
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py index 5257bd1..6f046ea 100755 --- a/scripts/from_genbank_to_fasta_and_yaml.py +++ b/scripts/from_genbank_to_fasta_and_yaml.py @@ -7,6 +7,8 @@ import xml.etree.ElementTree as ET import json import os +from dateutil import parser + num_ids_for_request = 100 dir_metadata = 'metadata_from_nuccore' @@ -37,20 +39,19 @@ if not os.path.exists(dir_metadata): tmp_list = [x.split('.')[0] for x in tmp_list] print(term, len(tmp_list)) - tmp_list=tmp_list - # tmp_list = tmp_list[0:2] # restricting to small run + #tmp_list = tmp_list[0:2] # restricting to small run id_set.update([x.split('.')[0] for x in tmp_list]) print(term_list, len(id_set)) - with open(path_ncbi_virus_accession) as f: - tmp_list = [line.strip('\n') for line in f] - - print('NCBI Virus', len(tmp_list)) - id_set.update(tmp_list) - - print(term_list + ['NCBI Virus'], len(id_set)) + if os.path.exists(path_ncbi_virus_accession): + with open(path_ncbi_virus_accession) as f: + tmp_list = [line.strip('\n') for line in f] + print('NCBI Virus', len(tmp_list)) + id_set.update(tmp_list) + term_list.append('NCBI Virus') + print(term_list, len(id_set)) for i, id_x_list in enumerate(chunks(list(id_set), num_ids_for_request)): path_metadata_xxx_xml = os.path.join(dir_metadata, 'metadata_{}.xml'.format(i)) @@ -86,7 +87,7 @@ if not os.path.exists(dir_fasta_and_yaml): os.makedirs(dir_fasta_and_yaml) 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')]: tree = ET.parse(path_metadata_xxx_xml) GBSet = tree.getroot() @@ -110,23 +111,23 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) 'submitter': {} } - + info_for_yaml_dict['sample']['sample_id'] = accession_version - info_for_yaml_dict['sample']['source_database_accession'] = accession_version - - + info_for_yaml_dict['sample']['source_database_accession'] = ["http://identifiers.org/insdc/"+accession_version+"#sequence"] #accession is turned into resolvable URL/URI now + + # submitter info GBSeq_references = GBSeq.find('GBSeq_references') if GBSeq_references is not None: - info_for_yaml_dict['submitter']['authors'] = ';'.join([x.text for x in GBSeq_references.iter('GBAuthor')]) - + info_for_yaml_dict['submitter']['authors'] = ["{}".format(x.text) for x in GBSeq_references.iter('GBAuthor')] + GBReference = GBSeq_references.find('GBReference') if GBReference is not None: GBReference_journal = GBReference.find('GBReference_journal') - + if GBReference_journal is not None and GBReference_journal.text != 'Unpublished': if 'Submitted' in GBReference_journal.text: - info_for_yaml_dict['submitter']['submitter_name'] = GBReference_journal.text.split(') ')[1].split(',')[0].strip() + info_for_yaml_dict['submitter']['submitter_name'] = ["{}".format(GBReference_journal.text.split(') ')[1].split(',')[0].strip())] info_for_yaml_dict['submitter']['submitter_address'] = ','.join(GBReference_journal.text.split(') ')[1].split(',')[1:]).strip() else: info_for_yaml_dict['submitter']['additional_submitter_information'] = GBReference_journal.text @@ -146,8 +147,9 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) if field_in_yaml == 'sequencing_coverage': # A regular expression would be better! try: - info_for_yaml_dict['technology'][field_in_yaml] = float( - tech_info_to_parse.strip('(average)').strip("reads/nt").strip('(average for 6 sequences)').replace(',', '.').strip(' xX>')) + info_for_yaml_dict['technology'][field_in_yaml] = [ + float(tech_info_to_parse.strip('(average)').strip("reads/nt").strip('(average for 6 sequences)').replace(',', '.').strip(' xX>')) + ] except ValueError: print(accession_version, "Couldn't make sense of Coverage '%s'" % tech_info_to_parse) pass @@ -162,8 +164,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) new_seq_tec_list.append(seq_tec) - for n, seq_tec in enumerate(new_seq_tec_list): - info_for_yaml_dict['technology'][field_in_yaml + ('' if n == 0 else str(n + 1))] = seq_tec + info_for_yaml_dict['technology']['sample_sequencing_technology'] = [x for x in new_seq_tec_list] else: info_for_yaml_dict['technology'][field_in_yaml] = tech_info_to_parse @@ -199,7 +200,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) if 'age' in GBQualifier_value_text: info_for_yaml_dict['host']['host_age'] = int(GBQualifier_value_text_list[2].split('age ')[1]) - info_for_yaml_dict['host']['host_age_unit'] = 'year' + info_for_yaml_dict['host']['host_age_unit'] = 'http://purl.obolibrary.org/obo/UO_0000036' 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 @@ -208,24 +209,46 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) elif GBQualifier_name_text == 'isolation_source': if GBQualifier_value_text.upper() in term_to_uri_dict: GBQualifier_value_text = GBQualifier_value_text.upper() # For example, in case of 'usa: wa' - + if GBQualifier_value_text in term_to_uri_dict: - info_for_yaml_dict['sample']['specimen_source'] = term_to_uri_dict[GBQualifier_value_text] + 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']: - info_for_yaml_dict['sample']['specimen_source'] = term_to_uri_dict['nasopharyngeal swab'] - info_for_yaml_dict['sample']['specimen_source2'] = term_to_uri_dict['oropharyngeal swab'] - elif GBQualifier_value_text in ['nasopharyngeal swab/throat swab']: - info_for_yaml_dict['sample']['specimen_source'] = term_to_uri_dict['nasopharyngeal swab'] - info_for_yaml_dict['sample']['specimen_source2'] = term_to_uri_dict['throat 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']: + 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'] - info_for_yaml_dict['sample']['specimen_source2'] = term_to_uri_dict['throat swab'] + info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal aspirate'], term_to_uri_dict['throat swab']] else: missing_value_list.append('\t'.join([accession_version, 'specimen_source', GBQualifier_value_text])) elif GBQualifier_name_text == 'collection_date': # TO_DO: which format we will use? - info_for_yaml_dict['sample']['collection_date'] = GBQualifier_value_text + date_to_write = GBQualifier_value_text + + if len(GBQualifier_value_text.split('-')) == 1: + if int(GBQualifier_value_text) < 2020: + date_to_write = "15 12 {}".format(GBQualifier_value_text) + else: + date_to_write = "15 01 {}".format(GBQualifier_value_text) + + if 'additional_collection_information' in info_for_yaml_dict['sample']: + info_for_yaml_dict['sample']['additional_collection_information'] += "; The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text) + else: + info_for_yaml_dict['sample']['additional_collection_information'] = "The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text) + elif len(GBQualifier_value_text.split('-')) == 2: + date_to_write += '-15' + + if 'additional_collection_information' in info_for_yaml_dict['sample']: + info_for_yaml_dict['sample']['additional_collection_information'] += "; The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text) + else: + info_for_yaml_dict['sample']['additional_collection_information'] = "The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text) + elif len(GBQualifier_value_text.split('-')) == 3: + GBQualifier_value_text_list = GBQualifier_value_text.split('-') + + if GBQualifier_value_text_list[1].isalpha(): + date_to_write = GBQualifier_value_text_list[1] + ' ' + GBQualifier_value_text_list[0] + ' ' + GBQualifier_value_text_list[2] + + info_for_yaml_dict['sample']['collection_date'] = date_to_write elif GBQualifier_name_text in ['lat_lon', 'country']: if GBQualifier_value_text == 'Hong Kong': GBQualifier_value_text = 'China: Hong Kong' @@ -237,7 +260,10 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) info_for_yaml_dict['sample']['collection_location'] = GBQualifier_value_text elif GBQualifier_name_text == 'note': - info_for_yaml_dict['sample']['additional_collection_information'] = GBQualifier_value_text + if 'additional_collection_information' in info_for_yaml_dict['sample']: + info_for_yaml_dict['sample']['additional_collection_information'] += '; ' + GBQualifier_value_text + else: + info_for_yaml_dict['sample']['additional_collection_information'] = GBQualifier_value_text elif GBQualifier_name_text == 'isolate': info_for_yaml_dict['virus']['virus_strain'] = GBQualifier_value_text elif GBQualifier_name_text == 'db_xref': @@ -254,7 +280,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) with open(os.path.join(dir_fasta_and_yaml, '{}.yaml'.format(accession_version)), 'w') as fw: json.dump(info_for_yaml_dict, fw, indent=2) - + if len(missing_value_list) > 0: with open('missing_terms.tsv', 'w') as fw: fw.write('\n'.join(missing_value_list)) |