diff options
Diffstat (limited to 'workflows/pull-data/genbank/transform_genbank2yamlfa.py')
| -rwxr-xr-x | workflows/pull-data/genbank/transform_genbank2yamlfa.py | 326 |
1 files changed, 0 insertions, 326 deletions
diff --git a/workflows/pull-data/genbank/transform_genbank2yamlfa.py b/workflows/pull-data/genbank/transform_genbank2yamlfa.py deleted file mode 100755 index 8b970b6..0000000 --- a/workflows/pull-data/genbank/transform_genbank2yamlfa.py +++ /dev/null @@ -1,326 +0,0 @@ -#!/usr/bin/env python3 -# -# Create a single YAML/FASTA from genbank XML - -# ---------------------------------------------------------------------- -""" -Generate metadata (YAML) and FASTA files for each accession -""" - -if not os.path.exists(dir_fasta_and_yaml): - os.makedirs(dir_fasta_and_yaml) - -min_len_to_count = 15000 -num_seq_with_len_ge_X_bp = 0 - -missing_value_list = [] -not_created_accession_dict = {} -accession_with_errors_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() - - for GBSeq in GBSet: - accession_version = GBSeq.find('GBSeq_accession-version').text - - GBSeq_sequence = GBSeq.find('GBSeq_sequence') - if GBSeq_sequence is None: - print(accession_version, ' - sequence not found') - continue - - try: - # print(path_metadata_xxx_xml, accession_version) - - # A general default-empty yaml could be read from the definitive one - info_for_yaml_dict = { - 'id': 'placeholder', - 'host': {}, - 'sample': {}, - 'virus': {}, - 'technology': {}, - 'submitter': {} - } - - - info_for_yaml_dict['sample']['sample_id'] = 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: - author_list = ["{}".format(x.text) for x in GBSeq_references.iter('GBAuthor')] - if len(author_list) > 0: - info_for_yaml_dict['submitter']['authors'] = author_list - - 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= GBReference.find('GBReference_journal') - - if GBReference_journal is not None and GBReference_journal.text != 'Unpublished': - if 'Submitted' in GBReference_journal.text: - info_for_yaml_dict['submitter']['submitter_name'] = ["{}".format(GBReference_journal.text.split(')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 - - # This script download and prepare data and metadata for assemblies samples - info_for_yaml_dict['technology']['assembly_method'] = 'http://purl.obolibrary.org/obo/GENEPIO_0001628' - - GBSeq_comment = GBSeq.find('GBSeq_comment') - if GBSeq_comment is not None and 'Assembly-Data' in GBSeq_comment.text: - prefix_split_string = '##Genome-Assembly' if GBSeq_comment.text.startswith('##Genome-') else '##Assembly' - - GBSeq_comment_text = GBSeq_comment.text.split( - '{}-Data-START## ; '.format(prefix_split_string) - )[1].split(' ; {}-Data-END##'.format(prefix_split_string))[0] - - for info_to_check, field_in_yaml in zip( - ['Assembly Method', 'Coverage', 'Sequencing Technology'], - ['alignment_protocol', 'sequencing_coverage', 'sample_sequencing_technology'] - ): - if info_to_check in GBSeq_comment_text: - tech_info_to_parse = GBSeq_comment_text.split('{} :: '.format(info_to_check))[1].split(' ;')[0] - - 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.replace('(average)', '').replace("reads/nt", ''). - replace('(average for 6 sequences)', '').replace(',', '.').strip(' xX>')) - ] - except ValueError: - print(accession_version, "Couldn't make sense of Coverage '%s'" % tech_info_to_parse) - pass - elif field_in_yaml == 'sample_sequencing_technology': - new_seq_tec_list = [] - for seq_tec in tech_info_to_parse.split(';'): - seq_tec = seq_tec.strip() - if seq_tec in field_to_term_to_uri_dict['ncbi_sequencing_technology']: - seq_tec = field_to_term_to_uri_dict['ncbi_sequencing_technology'][seq_tec] - new_seq_tec_list.append(seq_tec) - else: - missing_value_list.append('\t'.join([accession_version, 'sample_sequencing_technology', seq_tec])) - - if len(new_seq_tec_list) > 0: - 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 - - - for GBFeature in GBSeq.iter('GBFeature'): - if GBFeature.find('GBFeature_key').text != 'source': - continue - - for GBQualifier in GBFeature.iter('GBQualifier'): - GBQualifier_value = GBQualifier.find('GBQualifier_value') - if GBQualifier_value is None: - continue - GBQualifier_value_text = GBQualifier_value.text - - GBQualifier_name_text = GBQualifier.find('GBQualifier_name').text - - if GBQualifier_name_text == 'host': - GBQualifier_value_text = GBQualifier_value_text.split(';')[0] # For case like Homo sapiens;sex:female - if GBQualifier_value_text in field_to_term_to_uri_dict['ncbi_host_species']: - # Cases like 'Felis catus; Domestic Shorthair' - info_for_yaml_dict['host']['host_species'] = field_to_term_to_uri_dict['ncbi_host_species'][GBQualifier_value_text] - else: - GBQualifier_value_text_list = GBQualifier_value_text.split('; ') - - if GBQualifier_value_text_list[0] in field_to_term_to_uri_dict['ncbi_host_species']: - info_for_yaml_dict['host']['host_species'] = field_to_term_to_uri_dict['ncbi_host_species'][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'] = field_to_term_to_uri_dict['ncbi_host_species']['Canis lupus familiaris'] - 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: - 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 field_to_term_to_uri_dict['ncbi_host_health_status']: - info_for_yaml_dict['host']['host_health_status'] = field_to_term_to_uri_dict['ncbi_host_health_status'][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]])) - - # 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 host_age >= 0 and host_age < 110: - 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]])) - 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 - else: - info_for_yaml_dict['sample']['collector_name'] = GBQualifier_value_text - elif GBQualifier_name_text == 'isolation_source': - if GBQualifier_value_text.upper() in field_to_term_to_uri_dict['ncbi_speciesman_source']: - 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 field_to_term_to_uri_dict['ncbi_speciesman_source']: - info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source'][GBQualifier_value_text]] - else: - if GBQualifier_value_text.lower() in ['np/op', 'np-op', 'np/op swab', 'np/np swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'combined nasopharyngeal and oropharyngeal swab', 'naso and/or oropharyngeal swab']: - info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['oropharyngeal swab']] - elif GBQualifier_value_text.lower() in ['nasopharyngeal swab/throat swab', 'nasopharyngeal/throat swab', 'nasopharyngeal swab and throat swab', 'nasal swab and throat swab', 'nasopharyngeal aspirate/throat swab', 'Nasopharyngeal/Throat']: - info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['throat swab']] - elif GBQualifier_value_text.lower() in ['nasopharyngeal aspirate & throat swab', 'nasopharyngeal aspirate and throat swab']: - info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal aspirate'], field_to_term_to_uri_dict['ncbi_speciesman_source']['throat swab']] - elif GBQualifier_value_text.lower() in ['nasal swab and throat swab']: - info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['throat swab']] - elif GBQualifier_value_text.lower() in ['nasal-swab and oro-pharyngeal swab']: - info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['oropharyngeal 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? - date_to_write = GBQualifier_value_text - - if len(GBQualifier_value_text.split('-')) == 1: - if int(GBQualifier_value_text) < 2020: - date_to_write = "{}-12-15".format(GBQualifier_value_text) - else: - date_to_write = "{}-01-15".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 = parse(GBQualifier_value_text).strftime('%Y-%m') + '-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 = parse(GBQualifier_value_text).strftime('%Y-%m-%d') - - info_for_yaml_dict['sample']['collection_date'] = date_to_write - elif GBQualifier_name_text in ['lat_lon', 'country']: - if GBQualifier_name_text == 'country' and ': ' in GBQualifier_value_text: - GBQualifier_value_text = GBQualifier_value_text.replace(': ', ':') - - if GBQualifier_value_text in field_to_term_to_uri_dict['ncbi_countries']: - info_for_yaml_dict['sample']['collection_location'] = field_to_term_to_uri_dict['ncbi_countries'][GBQualifier_value_text] - else: - missing_value_list.append('\t'.join([accession_version, GBQualifier_name_text, GBQualifier_value_text])) - elif GBQualifier_name_text == 'note': - 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': - info_for_yaml_dict['virus']['virus_species'] = "http://purl.obolibrary.org/obo/NCBITaxon_"+GBQualifier_value_text.split('taxon:')[1] - - # Check if mandatory fields are missing - if 'sample_sequencing_technology' not in info_for_yaml_dict['technology']: - # print(accession_version, ' - technology not found') - if accession_version not in not_created_accession_dict: - not_created_accession_dict[accession_version] = [] - not_created_accession_dict[accession_version].append('sample_sequencing_technology not found') - - if 'collection_location' not in info_for_yaml_dict['sample']: - if accession_version not in not_created_accession_dict: - not_created_accession_dict[accession_version] = [] - not_created_accession_dict[accession_version].append('collection_location not found') - - if 'collection_date' not in info_for_yaml_dict['sample']: - if accession_version not in not_created_accession_dict: - not_created_accession_dict[accession_version] = [] - not_created_accession_dict[accession_version].append('collection_date not found') - else: - year, month, day = [int(x) for x in info_for_yaml_dict['sample']['collection_date'].split('-')] - - collection_date_in_yaml = datetime(year, month, day) - if collection_date_in_yaml < min_acceptable_collection_date: - if accession_version not in not_created_accession_dict: - not_created_accession_dict[accession_version] = [] - not_created_accession_dict[accession_version].append('collection_date too early') - - if 'authors' not in info_for_yaml_dict['submitter']: - if accession_version not in not_created_accession_dict: - not_created_accession_dict[accession_version] = [] - not_created_accession_dict[accession_version].append('authors not found') - - if 'host_species' not in info_for_yaml_dict['host']: - if accession_version not in not_created_accession_dict: - not_created_accession_dict[accession_version] = [] - not_created_accession_dict[accession_version].append('host_species not found') - - if len(GBSeq_sequence.text) < min_len_to_count: - if accession_version not in not_created_accession_dict: - not_created_accession_dict[accession_version] = [] - not_created_accession_dict[accession_version].append('sequence shorter than {} bp'.format(min_len_to_count)) - - if accession_version not in not_created_accession_dict: - num_seq_with_len_ge_X_bp += 1 - - with open(os.path.join(dir_fasta_and_yaml, '{}.fasta'.format(accession_version)), 'w') as fw: - fw.write('>{}\n{}'.format(accession_version, GBSeq_sequence.text.upper())) - - 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) - except: - print("Unexpected error for the ID {}: {}".format(accession_version, sys.exc_info()[0])) - accession_with_errors_list.append(accession_version) - continue - -if len(missing_value_list) > 0: - path_missing_terms_tsv = 'missing_terms.genbank.tsv' - print('Written missing terms in {}'.format(path_missing_terms_tsv)) - with open(path_missing_terms_tsv, 'w') as fw: - fw.write('\n'.join(missing_value_list)) - -if len(accession_with_errors_list) > 0: - path_accession_with_errors_tsv = 'accession_with_errors.genbank.tsv' - 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)) - -if len(not_created_accession_dict) > 0: - path_not_created_accession_tsv = 'not_created_accession.genbank.tsv' - print('Written not created accession in {}'.format(path_not_created_accession_tsv)) - with open(path_not_created_accession_tsv, 'w') as fw: - fw.write('\n'.join(['\t'.join([accession_version, ','.join(missing_info_list)]) for accession_version, missing_info_list in not_created_accession_dict.items()])) - -print('Num. new sequences with length >= {} bp: {}'.format(min_len_to_count, num_seq_with_len_ge_X_bp)) |