diff options
Diffstat (limited to 'scripts/from_genbank_to_fasta_and_yaml.py')
| -rw-r--r-- | scripts/from_genbank_to_fasta_and_yaml.py | 141 |
1 files changed, 141 insertions, 0 deletions
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py new file mode 100644 index 0000000..0cc1a57 --- /dev/null +++ b/scripts/from_genbank_to_fasta_and_yaml.py @@ -0,0 +1,141 @@ +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) |