diff options
Diffstat (limited to 'scripts/download_genbank_data')
| -rw-r--r-- | scripts/download_genbank_data/.gitignore | 3 | ||||
| -rw-r--r-- | scripts/download_genbank_data/.guix-run | 5 | ||||
| -rwxr-xr-x | scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py | 490 |
3 files changed, 0 insertions, 498 deletions
diff --git a/scripts/download_genbank_data/.gitignore b/scripts/download_genbank_data/.gitignore deleted file mode 100644 index 69b8a57..0000000 --- a/scripts/download_genbank_data/.gitignore +++ /dev/null @@ -1,3 +0,0 @@ -fasta_and_yaml/ -*.tsv -*.acc diff --git a/scripts/download_genbank_data/.guix-run b/scripts/download_genbank_data/.guix-run deleted file mode 100644 index 1403c69..0000000 --- a/scripts/download_genbank_data/.guix-run +++ /dev/null @@ -1,5 +0,0 @@ -#!/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/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py deleted file mode 100755 index 9b2c9eb..0000000 --- a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py +++ /dev/null @@ -1,490 +0,0 @@ -#!/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)) |