diff options
Diffstat (limited to 'workflows/pull-data/genbank')
| -rw-r--r-- | workflows/pull-data/genbank/.gitignore | 3 | ||||
| -rw-r--r-- | workflows/pull-data/genbank/.guix-run | 5 | ||||
| -rwxr-xr-x | workflows/pull-data/genbank/from_genbank_to_fasta_and_yaml.py | 490 |
3 files changed, 498 insertions, 0 deletions
diff --git a/workflows/pull-data/genbank/.gitignore b/workflows/pull-data/genbank/.gitignore new file mode 100644 index 0000000..69b8a57 --- /dev/null +++ b/workflows/pull-data/genbank/.gitignore @@ -0,0 +1,3 @@ +fasta_and_yaml/ +*.tsv +*.acc diff --git a/workflows/pull-data/genbank/.guix-run b/workflows/pull-data/genbank/.guix-run new file mode 100644 index 0000000..1403c69 --- /dev/null +++ b/workflows/pull-data/genbank/.guix-run @@ -0,0 +1,5 @@ +#!/bin/sh +# Runner + +echo python3 from_genbank_to_fasta_and_yaml.py +guix environment guix --ad-hoc python python-biopython python-requests python-dateutil diff --git a/workflows/pull-data/genbank/from_genbank_to_fasta_and_yaml.py b/workflows/pull-data/genbank/from_genbank_to_fasta_and_yaml.py new file mode 100755 index 0000000..9b2c9eb --- /dev/null +++ b/workflows/pull-data/genbank/from_genbank_to_fasta_and_yaml.py @@ -0,0 +1,490 @@ +#!/usr/bin/env python3 +# +# - bulk download genbank data and matadata, preparing the FASTA and +# the YAML files +# +# See .guix-run python3 from_genbank_to_fasta_and_yaml.py + +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))) + + +# ---------------------------------------------------------------------- +""" +With --only-missing-ids only download accessions that we do not yet have! +""" +accession_already_downloaded_set = set() + +if os.path.exists(dir_fasta_and_yaml): + """ + If the fasta_and_yaml directory exists and --only-missing-ids was set + we make a list of all downloaded accessions: + """ + 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) + + """ + Fetch all YAML filenames and load `accession_already_downloaded_set` + """ + 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) + +# ---------------------------------------------------------------------- +""" +Check for --ids-to-consider +""" +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))) + +# ---------------------------------------------------------------------- +""" +Download section for genbank XML +""" + +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() + ) + +# ---------------------------------------------------------------------- +""" +Generate metadata (YAML) and FASTA files for each accession +""" + + +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.replace('(average)', '').replace("reads/nt", ''). + replace('(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 >= 0 and host_age < 110: + 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 = parse(GBQualifier_value_text).strftime('%Y-%m') + '-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)) |