diff options
| -rw-r--r-- | workflows/pull-data/genbank/genbank.py | 36 | ||||
| -rw-r--r-- | workflows/pull-data/genbank/ref.py | 237 |
2 files changed, 66 insertions, 207 deletions
diff --git a/workflows/pull-data/genbank/genbank.py b/workflows/pull-data/genbank/genbank.py index 90f5a14..80432de 100644 --- a/workflows/pull-data/genbank/genbank.py +++ b/workflows/pull-data/genbank/genbank.py @@ -52,18 +52,28 @@ Example of an output JSON: } } -Note: missing data should be None! Do not fill in other data by -'guessing'. - -When data is malformed an warning should be issued. """ def get_metadata(id, gbseq): + """This is a minimal data parser from genbank XML records. Inference + on, for example geo location, is not allowed in this function and + happens downstream. + + That is to keep the parsing simple. + + Important: missing data should be missing or None! Do not fill in + data by 'guessing'. + + When data is malformed a warning should be logged and added to the + warning list. + + """ host = types.SimpleNamespace() sample = types.SimpleNamespace() submitter = types.SimpleNamespace() technology = types.SimpleNamespace() + virus = types.SimpleNamespace() warnings = [] def warn(msg): @@ -81,13 +91,14 @@ def get_metadata(id, gbseq): sample.sample_id = id sample.database = "https://www.ncbi.nlm.nih.gov/genbank/" sample.source_database_accession = f"http://identifiers.org/insdc/{id}#sequence" - # <GBQualifier> - # <GBQualifier_name>country</GBQualifier_name> # <GBQualifier_value>USA: Cruise_Ship_1, California</GBQualifier_value> - # </GBQualifier> - sample.collection_location = "FIXME" + n = fetch("host_species", ".//GBQualifier/GBQualifier_name/[.='country']/../GBQualifier_value") + if n: sample.collection_location = n + else: warn("Missing collection_location") submitter.authors = [n.text for n in gbseq.findall(".//GBAuthor")] + if not len(submitter.authors): warn("Missing authors") + # <GBReference_journal>Submitted (28-OCT-2020) MDU-PHL, The Peter # Doherty Institute for Infection and Immunity, 792 Elizabeth # Street, Melbourne, Vic 3000, Australia @@ -103,7 +114,6 @@ def get_metadata(id, gbseq): pass except ValueError: submitter.additional_submitter_information = n - pass try: n = gbseq.find("./GBSeq_comment").text @@ -122,6 +132,7 @@ def get_metadata(id, gbseq): p = re.compile(r'.*Sequencing Technology :: ([^;]+).*') m = p.match(n) if m: technology.sample_sequencing_technology = m.group(1).strip() + else: warn("Missing sample_sequencing_technology") # --- Dates n = gbseq.find("./GBSeq_create-date") @@ -171,13 +182,18 @@ def get_metadata(id, gbseq): host.host_age = int(m.group(1)) host.host_age_unit = 'http://purl.obolibrary.org/obo/UO_0000036' # sys.exit(1) + n = fetch("virus_strain", ".//GBQualifier/GBQualifier_name/[.='isolate']/../GBQualifier_value") + if n: virus.virus_strain = n + n = fetch("virus_species", ".//GBQualifier/GBQualifier_name/[.='db_xref']/../GBQualifier_value") + if n: virus.virus_species = "http://purl.obolibrary.org/obo/NCBITaxon_"+n.split('taxon:')[1] + info = { 'id': 'placeholder', 'update_date': str(update_date), 'host': host.__dict__, 'sample': sample.__dict__, - #'virus': virus, + 'virus': virus.__dict__, 'technology': technology.__dict__, 'submitter': submitter.__dict__, 'warnings': warnings, diff --git a/workflows/pull-data/genbank/ref.py b/workflows/pull-data/genbank/ref.py index a9b4f06..4d4df48 100644 --- a/workflows/pull-data/genbank/ref.py +++ b/workflows/pull-data/genbank/ref.py @@ -1,199 +1,42 @@ # ---- BELOW IS JUST FOR REFERENCE ---- - if field_in_yaml == 'sequencing_coverage': - # A regular expression would be better! - try: - 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: - technology['sample_sequencing_technology'] = [x for x in new_seq_tec_list] - else: - technology[field_in_yaml] = tech_info_to_parse - - - - - 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']: - 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']: - 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: - host['host_age'] = host_age - 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']]): - sample['collecting_institution'] = GBQualifier_value_text - else: - 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']: - 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']: - 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']: - 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']: - 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']: - 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']: - 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 sample: - sample['additional_collection_information'] += "; The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text) - else: - 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 sample: - sample['additional_collection_information'] += "; The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text) - else: - 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') - - 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']: - 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 sample: - sample['additional_collection_information'] += '; ' + GBQualifier_value_text - else: - sample['additional_collection_information'] = GBQualifier_value_text - elif GBQualifier_name_text == 'isolate': - virus['virus_strain'] = GBQualifier_value_text - elif GBQualifier_name_text == 'db_xref': - 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 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 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 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 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 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 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, 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)) +if field_in_yaml == 'sequencing_coverage': + # A regular expression would be better! + try: + 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 GBQualifier_name_text == 'collected_by': + if any([x in GBQualifier_value_text.lower() for x in ['institute', 'hospital', 'city', 'center']]): + sample['collecting_institution'] = GBQualifier_value_text + else: + 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']: + 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']: + 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']: + 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']: + 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']: + 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']: + 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])) |