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