#!/usr/bin/env python3 import argparse parser = argparse.ArgumentParser() parser.add_argument('--ids-to-ignore', type=str, help='file with ids to ignore in all steps, 1 id per line', required=False) parser.add_argument('--ids-to-consider', type=str, help='file with ids to consider in all steps, 1 id per line', required=False) parser.add_argument('--skip-request', action='store_true', help='skip metadata and sequence request', required=False) parser.add_argument('--only-missing-ids', action='store_true', help='download only missing ids not already downloaded', required=False) parser.add_argument('--dict-ontology', type=str, help='where is the ontology', default='../dict_ontology_standardization/', required=False) args = parser.parse_args() from Bio import Entrez Entrez.email = 'another_email@gmail.com' import xml.etree.ElementTree as ET import json import os import requests from datetime import date, datetime from dateutil.parser import parse import sys sys.path.append('../') from utils import is_integer, chunks, check_and_get_ontology_dictionaries num_ids_for_request = 100 min_acceptable_collection_date = datetime(2019, 12, 1) dir_metadata = 'metadata_from_nuccore' dir_fasta_and_yaml = 'fasta_and_yaml' dir_dict_ontology_standardization = args.dict_ontology today_date = date.today().strftime("%Y.%m.%d") path_ncbi_virus_accession = 'sequences.{}.acc'.format(today_date) field_to_term_to_uri_dict = check_and_get_ontology_dictionaries(dir_dict_ontology_standardization) if os.path.exists(dir_metadata): print("The directory '{}' already exists.".format(dir_metadata)) if not args.skip_request: print("\tTo start the request, delete the directory '{}' or specify --skip-request.".format(dir_metadata)) sys.exit(-1) accession_to_ignore_set = set() if args.ids_to_ignore: if not os.path.exists(args.ids_to_ignore): print("\tThe '{}' file doesn't exist.".format(args.ids_to_ignore)) sys.exit(-1) with open(args.ids_to_ignore) as f: accession_to_ignore_set.update(set([x.split('.')[0] for x in f.read().strip('\n').split('\n')])) print('There are {} accessions to ignore.'.format(len(accession_to_ignore_set))) accession_already_downloaded_set = set() if os.path.exists(dir_fasta_and_yaml): print("The directory '{}' already exists.".format(dir_fasta_and_yaml)) if not args.only_missing_ids: print("To start the download, delete the directory '{}' or specify --only-missing-ids.".format(dir_fasta_and_yaml)) sys.exit(-1) accession_already_downloaded_set = set([x.split('.yaml')[0].split('.')[0] for x in os.listdir(dir_fasta_and_yaml) if x.endswith('.yaml')]) print('There are {} accessions already downloaded.'.format(len(accession_already_downloaded_set))) accession_to_ignore_set.update(accession_already_downloaded_set) accession_to_consider_set = set() if args.ids_to_consider: if not os.path.exists(args.ids_to_consider): print("\tThe '{}' file doesn't exist.".format(args.ids_to_consider)) sys.exit(-1) with open(args.ids_to_consider) as f: accession_to_consider_set.update(set([x.split('.')[0] for x in f.read().strip('\n').split('\n')])) if len(accession_to_consider_set) > 0: print('There are {} accessions to consider.'.format(len(accession_to_consider_set))) if not os.path.exists(dir_metadata): # Take all the ids id_set = set() # Try to search several strings 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'] # Remove mRNAs, ncRNAs, Proteins, and predicted models (more information here: https://en.wikipedia.org/wiki/RefSeq) # Remove the version in the id new_ids_set = set([x.split('.')[0] for x in tmp_list if x[:2] not in ['NM', 'NR', 'NP', 'XM', 'XR', 'XP', 'WP']]) if len(accession_to_consider_set) > 0: new_ids_set = new_ids_set.intersection(accession_to_consider_set) new_ids = len(new_ids_set.difference(id_set)) id_set.update(new_ids_set) print('Term:', term, '-->', new_ids, 'new IDs from', len(tmp_list), '---> Total unique IDs:', len(id_set)) if not os.path.exists(path_ncbi_virus_accession): r = requests.get('https://www.ncbi.nlm.nih.gov/genomes/VirusVariation/vvsearch2/?q=*:*&fq=%7B!tag=SeqType_s%7DSeqType_s:(%22Nucleotide%22)&fq=VirusLineageId_ss:(2697049)&cmd=download&sort=SourceDB_s%20desc,CreateDate_dt%20desc,id%20asc&dlfmt=acc&fl=id') with open(path_ncbi_virus_accession, 'w') as fw: fw.write(r.text) with open(path_ncbi_virus_accession) as f: tmp_list = [line.strip('\n') for line in f] new_ids_set = set(tmp_list) if len(accession_to_consider_set) > 0: new_ids_set = new_ids_set.intersection(accession_to_consider_set) new_ids = len(new_ids_set.difference(id_set)) id_set.update(new_ids_set) print('DB: NCBI Virus', today_date, '-->', new_ids, 'new IDs from', len(tmp_list), '---> Total unique IDs:', len(id_set)) id_set = id_set.difference(accession_to_ignore_set) print('There are {} missing IDs to download.'.format(len(id_set))) os.makedirs(dir_metadata) for i, id_x_list in enumerate(chunks(list(id_set), num_ids_for_request)): path_metadata_xxx_xml = os.path.join(dir_metadata, 'metadata_{}.xml'.format(i)) print('Requesting {} ids --> {}'.format(len(id_x_list), path_metadata_xxx_xml)) with open(path_metadata_xxx_xml, 'w') as fw: fw.write( Entrez.efetch(db='nuccore', id=id_x_list, retmode='xml').read() ) if not os.path.exists(dir_fasta_and_yaml): os.makedirs(dir_fasta_and_yaml) min_len_to_count = 15000 num_seq_with_len_ge_X_bp = 0 missing_value_list = [] not_created_accession_dict = {} accession_with_errors_list = [] for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) for name_metadata_xxx_xml in os.listdir(dir_metadata) if name_metadata_xxx_xml.endswith('.xml')]: tree = ET.parse(path_metadata_xxx_xml) GBSet = tree.getroot() 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 try: # print(path_metadata_xxx_xml, accession_version) # 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['sample']['source_database_accession'] = ["http://identifiers.org/insdc/"+accession_version+"#sequence"] #accession is turned into resolvable URL/URI now # submitter info GBSeq_references = GBSeq.find('GBSeq_references') if GBSeq_references is not None: author_list = ["{}".format(x.text) for x in GBSeq_references.iter('GBAuthor')] if len(author_list) > 0: info_for_yaml_dict['submitter']['authors'] = author_list GBReference = GBSeq_references.find('GBReference') if GBReference is not None: GBReference_journal = GBReference.find('GBReference_journal') if GBReference_journal is not None and GBReference_journal.text != 'Unpublished': if 'Submitted' in GBReference_journal.text: info_for_yaml_dict['submitter']['submitter_name'] = ["{}".format(GBReference_journal.text.split(') ')[1].split(',')[0].strip())] info_for_yaml_dict['submitter']['submitter_address'] = ','.join(GBReference_journal.text.split(') ')[1].split(',')[1:]).strip() else: info_for_yaml_dict['submitter']['additional_submitter_information'] = GBReference_journal.text # This script download and prepare data and metadata for assemblies samples info_for_yaml_dict['technology']['assembly_method'] = 'http://purl.obolibrary.org/obo/GENEPIO_0001628' GBSeq_comment = GBSeq.find('GBSeq_comment') if GBSeq_comment is not None and 'Assembly-Data' in GBSeq_comment.text: prefix_split_string = '##Genome-Assembly' if GBSeq_comment.text.startswith('##Genome-') else '##Assembly' GBSeq_comment_text = GBSeq_comment.text.split( '{}-Data-START## ; '.format(prefix_split_string) )[1].split(' ; {}-Data-END##'.format(prefix_split_string))[0] for info_to_check, field_in_yaml in zip( ['Assembly Method', 'Coverage', 'Sequencing Technology'], ['alignment_protocol', '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! try: info_for_yaml_dict['technology'][field_in_yaml] = [ float(tech_info_to_parse.strip('(average)').strip("reads/nt").strip('(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: info_for_yaml_dict['technology']['sample_sequencing_technology'] = [x for x in new_seq_tec_list] else: info_for_yaml_dict['technology'][field_in_yaml] = tech_info_to_parse 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 = GBQualifier_value_text.split(';')[0] # For case like Homo sapiens;sex:female if GBQualifier_value_text in field_to_term_to_uri_dict['ncbi_host_species']: # Cases like 'Felis catus; Domestic Shorthair' info_for_yaml_dict['host']['host_species'] = field_to_term_to_uri_dict['ncbi_host_species'][GBQualifier_value_text] else: GBQualifier_value_text_list = GBQualifier_value_text.split('; ') if GBQualifier_value_text_list[0] in field_to_term_to_uri_dict['ncbi_host_species']: info_for_yaml_dict['host']['host_species'] = field_to_term_to_uri_dict['ncbi_host_species'][GBQualifier_value_text_list[0]] elif GBQualifier_value_text_list[0] and ('MT215193' in accession_version or 'MT270814' in accession_version): # Information checked manually from NCBI Virus info_for_yaml_dict['host']['host_species'] = field_to_term_to_uri_dict['ncbi_host_species']['Canis lupus familiaris'] else: missing_value_list.append('\t'.join([accession_version, 'host_species', GBQualifier_value_text_list[0]])) # Possible cases: # - Homo sapiens --> ['Homo sapiens'] # - Homo sapiens; female --> ['Homo sapiens', 'female'] # - Homo sapiens; female 63 --> ['Homo sapiens', 'female 63'] # - Homo sapiens; female; age 40 --> ['Homo sapiens', 'female', 'age 40'] # - Homo sapiens; gender: F; age: 61 --> ['Homo sapiens', 'gender: F', 'age: 61'] # - Homo sapiens; gender: M; age: 68 --> ['Homo sapiens', 'gender: M', 'age: 68'] # - Homo sapiens; hospitalized patient --> ['Homo sapiens', 'hospitalized patient'] # - Homo sapiens; male --> ['Homo sapiens', 'male'] # - Homo sapiens; male; 63 --> ['Homo sapiens', 'male', '63'] # - Homo sapiens; male; age 29 --> ['Homo sapiens', 'male', 'age 29'] # - Homo sapiens; symptomatic --> ['Homo sapiens', 'symptomatic'] if len(GBQualifier_value_text_list) > 1: host_sex = '' if 'female' in GBQualifier_value_text_list[1]: host_sex = 'female' elif 'male' in GBQualifier_value_text_list[1]: host_sex = 'male' 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']: info_for_yaml_dict['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']: info_for_yaml_dict['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 > -1: info_for_yaml_dict['host']['host_age'] = host_age info_for_yaml_dict['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']]): 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.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']: info_for_yaml_dict['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']: info_for_yaml_dict['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']: info_for_yaml_dict['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']: info_for_yaml_dict['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']: info_for_yaml_dict['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']: info_for_yaml_dict['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 info_for_yaml_dict['sample']: info_for_yaml_dict['sample']['additional_collection_information'] += "; The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text) else: info_for_yaml_dict['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 += '-15' if 'additional_collection_information' in info_for_yaml_dict['sample']: info_for_yaml_dict['sample']['additional_collection_information'] += "; The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text) else: info_for_yaml_dict['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') info_for_yaml_dict['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']: info_for_yaml_dict['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 info_for_yaml_dict['sample']: info_for_yaml_dict['sample']['additional_collection_information'] += '; ' + GBQualifier_value_text else: 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'] = "http://purl.obolibrary.org/obo/NCBITaxon_"+GBQualifier_value_text.split('taxon:')[1] # Check if mandatory fields are missing if 'sample_sequencing_technology' not in info_for_yaml_dict['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 info_for_yaml_dict['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 info_for_yaml_dict['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 info_for_yaml_dict['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 info_for_yaml_dict['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 info_for_yaml_dict['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_for_yaml_dict, 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))