From 3bee6777fb4a61febbf1c22e62d71d933cfba4b0 Mon Sep 17 00:00:00 2001 From: Andrea Guarracino Date: Sat, 18 Apr 2020 22:15:01 +0200 Subject: new script release - now the script is more gentle with the server, requesting metadata in batches, reducing the ovrall execution time; - in the YAML files are created field for sample_sequencing_technology, sample_sequencing_technology2, sample_sequencing_technology3, specimen_source, and specimen_source2; - in sequencing_coverage stuff like 'x', 'X', etc... is stripped, and the ',' replaced by '.'; - the script exploits the dictionaries in the /scripts/dict_ontology_standardization. Now I have used ncbi_specesman_source.csv, ncbi_sequencing_technology.csv, and ncbi_countries.csv. - in ncbi_sequencing_technology.csv I've added 'Oxford Nanopore' and 'MinION Oxford Nanopore' - for specimen_source, when there is one of 'NP/OP swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', or 'np/np swab', I put both of them.--- scripts/from_genbank_to_fasta_and_yaml.py | 270 +++++++++++++++++++----------- 1 file changed, 170 insertions(+), 100 deletions(-) (limited to 'scripts') diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py index 0cc1a57..a7c9dc2 100644 --- a/scripts/from_genbank_to_fasta_and_yaml.py +++ b/scripts/from_genbank_to_fasta_and_yaml.py @@ -1,15 +1,19 @@ from Bio import Entrez -Entrez.email = 'your_email_to_be_polite' +Entrez.email = 'andresguarahino@gmail.com' import xml.etree.ElementTree as ET import yaml import os -path_ncbi_virus_accession = 'sequences.acc' +from datetime import date +today = date.today().strftime("%Y%m%d") + +dir_metadata_today = 'metadata_from_nuccore_{}'.format(today) +dir_fasta_and_yaml_today = 'fasta_and_yaml_{}'.format(today) -date = '20200414' -path_seq_fasta = 'seq_from_nuccore.{}.fasta'.format(date) -path_metadata_xml = 'metadata_from_nuccore.{}.xml'.format(date) +dir_dict_ontology_standardization = 'dict_ontology_standardization/' + +path_ncbi_virus_accession = 'sequences.acc' # Take all the ids id_set = set() @@ -19,9 +23,15 @@ for term in term_list: tmp_list = Entrez.read( Entrez.esearch(db='nuccore', term=term, idtype='acc', retmax='10000') )['IdList'] - print(term, len(tmp_list)) - + + # Remove mRNAs, ncRNAs, Proteins, and predicted models (more information here: https://en.wikipedia.org/wiki/RefSeq) + tmp_list = [x for x in tmp_list if x[:2] not in ['NM', 'NR', 'NP', 'XM', 'XR', 'XP', 'WP']] + # Remove the version in the id + tmp_list = [x.split('.')[0] for x in tmp_list] + + print(term, len(tmp_list)) + id_set.update([x.split('.')[0] for x in tmp_list]) print(term_list, len(id_set)) @@ -34,108 +44,168 @@ id_set.update(tmp_list) print(term_list + ['NCBI Virus'], len(id_set)) -if not os.path.exists(path_metadata_xml): - # TO_DO: to check if I already have the records? - - with open(path_metadata_xml, 'w') as fw: - fw.write( - Entrez.efetch(db='nuccore', id=list(id_set), retmode='xml').read() - ) - +def chunks(lst, n): + for i in range(0, len(lst), n): + yield lst[i:i + n] -tree = ET.parse(path_metadata_xml) -GBSet = tree.getroot() +num_ids_for_request = 100 +if not os.path.exists(dir_metadata_today): + os.makedirs(dir_metadata_today) + + for i, id_x_list in enumerate(chunks(list(id_set), num_ids_for_request)): + path_metadata_xxx_xml = os.path.join(dir_metadata_today, 'metadata_{}.xml'.format(i)) + print('Requesting {} ids --> {}'.format(len(id_x_list), path_metadata_xml)) + + with open(path_metadata_xxx_xml, 'w') as fw: + fw.write( + 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')]: + print('Read {}'.format(path_dict_xxx_csv)) + + with open(path_dict_xxx_csv) as f: + for line in f: + term, uri = line.strip('\n').split(',') + + term_to_uri_dict[term] = uri species_to_taxid_dict = { 'Homo sapiens': 9606 } -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 +if os.path.exists(dir_fasta_and_yaml_today): + os.makedirs(dir_fasta_and_yaml_today) - # A general default-empty yaml could be read from the definitive one - info_for_yaml_dict = { - 'id': 'placeholder', - 'host': {}, - 'sample': {}, - 'virus': {}, - 'technology': {}, - 'submitter': {} - } - + for path_metadata_xxx_xml in [os.path.join(dir_metadata_today, name_metadata_xxx_xml) for name_metadata_xxx_xml in os.listdir(dir_metadata_today) if name_metadata_xxx_xml.endswith('.xml')]: + tree = ET.parse(path_metadata_xxx_xml) + GBSet = tree.getroot() - info_for_yaml_dict['sample']['sample_id'] = accession_version - info_for_yaml_dict['submitter']['authors'] = ';'.join([x.text for x in GBSeq.iter('GBAuthor')]) + for GBSeq in GBSet: + accession_version = GBSeq.find('GBSeq_accession-version').text - - GBSeq_comment = GBSeq.find('GBSeq_comment') - if GBSeq_comment is not None and 'Assembly-Data' in GBSeq_comment.text: - GBSeq_comment_text = GBSeq_comment.text.split('##Assembly-Data-START## ; ')[1].split(' ; ##Assembly-Data-END##')[0] - - for info_to_check, field_in_yaml in zip( - ['Assembly Method', 'Coverage', 'Sequencing Technology'], - ['sequence_assembly_method', 'sequencing_coverage', 'sample_sequencing_technology'] - ): - if info_to_check in GBSeq_comment_text: - info_for_yaml_dict['technology'][field_in_yaml] = GBSeq_comment_text.split('{} :: '.format(info_to_check))[1].split(' ;')[0] - - - 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: + GBSeq_sequence = GBSeq.find('GBSeq_sequence') + if GBSeq_sequence is None: + print(accession_version, ' - sequence not found') continue - GBQualifier_value_text = GBQualifier_value.text - - GBQualifier_name_text = GBQualifier.find('GBQualifier_name').text - - if GBQualifier_name_text == 'host': - GBQualifier_value_text_list = GBQualifier_value_text.split('; ') - - info_for_yaml_dict['host']['host_common_name'] = GBQualifier_value_text_list[0] - - 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]] - - if len(GBQualifier_value_text_list) > 1: - if GBQualifier_value_text_list[1] in ['male', 'female']: - info_for_yaml_dict['host']['host_sex'] = GBQualifier_value_text_list[1] - else: - info_for_yaml_dict['host']['host_health_status'] = GBQualifier_value_text_list[1] - - 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' - 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': - info_for_yaml_dict['sample']['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 - elif GBQualifier_name_text in ['lat_lon', 'country']: - 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 - 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'] = int(GBQualifier_value_text.split('taxon:')[1]) - - with open('{}.fasta'.format(accession_version), 'w') as fw: - fw.write('>{}\n{}'.format(accession_version, GBSeq_sequence.text.upper())) - with open('{}.yaml'.format(accession_version), 'w') as fw: - yaml.dump(info_for_yaml_dict, fw, default_flow_style=False) + + # 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['submitter']['authors'] = ';'.join([x.text for x in GBSeq.iter('GBAuthor')]) + + + GBSeq_comment = GBSeq.find('GBSeq_comment') + if GBSeq_comment is not None and 'Assembly-Data' in GBSeq_comment.text: + GBSeq_comment_text = GBSeq_comment.text.split('##Assembly-Data-START## ; ')[1].split(' ; ##Assembly-Data-END##')[0] + + for info_to_check, field_in_yaml in zip( + ['Assembly Method', 'Coverage', 'Sequencing Technology'], + ['sequence_assembly_method', '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! + info_for_yaml_dict['technology'][field_in_yaml] = ';'.join( + [x.strip('(average)').strip("reads/nt").replace(',', '.').strip(' xX>') for x in tech_info_to_parse.split(';')] + ) + 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 term_to_uri_dict: + seq_tec = term_to_uri_dict[seq_tec] + else: + print(accession_version, 'missing technologies:', seq_tec) + + 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 + else: + info_for_yaml_dict['technology'][field_in_yaml] = tech_info_to_parse + + + #term_to_uri_dict + + 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_list = GBQualifier_value_text.split('; ') + + info_for_yaml_dict['host']['host_common_name'] = GBQualifier_value_text_list[0] + + 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]] + + if len(GBQualifier_value_text_list) > 1: + if GBQualifier_value_text_list[1] in ['male', 'female']: + info_for_yaml_dict['host']['host_sex'] = GBQualifier_value_text_list[1] + else: + info_for_yaml_dict['host']['host_health_status'] = GBQualifier_value_text_list[1] + + 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' + 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 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']: + 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'] + else: + print(accession_version, 'missing 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 + elif GBQualifier_name_text in ['lat_lon', 'country']: + if GBQualifier_value_text in term_to_uri_dict: + GBQualifier_value_text = term_to_uri_dict[GBQualifier_value_text] + else: + print(accession_version, 'missing {}:'.format(GBQualifier_name_text), GBQualifier_value_text) + + 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 + 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'] = int(GBQualifier_value_text.split('taxon:')[1]) + + with open(os.path.join(dir_fasta_and_yaml_today, '{}.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_today, '{}.yaml'.format(accession_version)), 'w') as fw: + yaml.dump(info_for_yaml_dict, fw, default_flow_style=False) -- cgit v1.2.3