from Bio import Entrez Entrez.email = 'your_email_to_be_polite' import xml.etree.ElementTree as ET import yaml import os path_ncbi_virus_accession = 'sequences.acc' date = '20200414' path_seq_fasta = 'seq_from_nuccore.{}.fasta'.format(date) path_metadata_xml = 'metadata_from_nuccore.{}.xml'.format(date) # Take all the ids id_set = set() term_list = ['SARS-CoV-2', 'SARS-CoV2', 'SARS CoV2', 'SARSCoV2', 'txid2697049[Organism]'] 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 the version in the id 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 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() ) tree = ET.parse(path_metadata_xml) GBSet = tree.getroot() 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 # 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: 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: 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)