diff options
Diffstat (limited to 'workflows/pull-data/genbank')
| -rwxr-xr-x | workflows/pull-data/genbank/genbank_pull.py | 166 | ||||
| -rw-r--r--[-rwxr-xr-x] | workflows/pull-data/genbank/transform_genbank2yamlfa.py (renamed from workflows/pull-data/genbank/from_genbank_to_fasta_and_yaml.py) | 167 |
2 files changed, 166 insertions, 167 deletions
diff --git a/workflows/pull-data/genbank/genbank_pull.py b/workflows/pull-data/genbank/genbank_pull.py new file mode 100755 index 0000000..07bb15d --- /dev/null +++ b/workflows/pull-data/genbank/genbank_pull.py @@ -0,0 +1,166 @@ +#!/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() + ) diff --git a/workflows/pull-data/genbank/from_genbank_to_fasta_and_yaml.py b/workflows/pull-data/genbank/transform_genbank2yamlfa.py index 9b2c9eb..025b4d9 100755..100644 --- a/workflows/pull-data/genbank/from_genbank_to_fasta_and_yaml.py +++ b/workflows/pull-data/genbank/transform_genbank2yamlfa.py @@ -1,170 +1,3 @@ -#!/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 |