diff options
Diffstat (limited to 'workflows/pull-data/genbank/update-from-genbank.py')
| -rwxr-xr-x | workflows/pull-data/genbank/update-from-genbank.py | 206 |
1 files changed, 77 insertions, 129 deletions
diff --git a/workflows/pull-data/genbank/update-from-genbank.py b/workflows/pull-data/genbank/update-from-genbank.py index 132f553..e62a611 100755 --- a/workflows/pull-data/genbank/update-from-genbank.py +++ b/workflows/pull-data/genbank/update-from-genbank.py @@ -3,20 +3,21 @@ # - bulk download genbank data and matadata, preparing the FASTA and # the YAML files # -# See .guix-run +# update-from-genbank.py --max 10 --skip ids.txt --outdir ~/tmp/genbank +# +# See directory .guix-run and README.md + +BATCH_SIZE=5000 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) +parser.add_argument('--max', type=int, help='Max queries', required=False) +parser.add_argument('--skip', type=str, help='File with ids to skip, 1 id per line', required=False) +parser.add_argument('--outdir', type=str, help='Output directory', required=True) args = parser.parse_args() from Bio import Entrez -Entrez.email = 'another_email@gmail.com' +Entrez.email = 'another_email@gmail.com' # FIXME import xml.etree.ElementTree as ET import json @@ -27,140 +28,87 @@ from datetime import date, datetime from dateutil.parser import parse import sys -sys.path.append('../') +# sys.path.append('../') from utils import is_integer, chunks, check_and_get_ontology_dictionaries - -num_ids_for_request = 100 +num_ids_for_request = 100 # batch calls 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 +outdir = args.outdir today_date = date.today().strftime("%Y.%m.%d") path_ncbi_virus_accession = 'sequences.{}.acc'.format(today_date) +if not os.path.exists(outdir): + raise Exception(f"Output directory {outdir} does not exist!") -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))) +skip = set() +if args.skip: + with open(args.skip) as f: + content = f.readlines() + for line in content: + skip.add(line.strip()) - -# ---------------------------------------------------------------------- -""" -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))) +print(f"Skip size is {len(skip)}",file=sys.stderr) # ---------------------------------------------------------------------- """ 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() - ) +# Try to search several strings +TERMS = ['SARS-CoV-2', 'SARS-CoV2', 'SARS CoV2', 'SARSCoV2', 'txid2697049[Organism]'] +# Remove mRNAs, ncRNAs, Proteins, and predicted models (more information here: https://en.wikipedia.org/wiki/RefSeq) starting with +PREFIX = ['NM', 'NR', 'NP', 'XM', 'XR', 'XP', 'WP'] + +ids = set() +for term in TERMS: + num_read = BATCH_SIZE + retstart = 0 + while num_read == BATCH_SIZE: + record = Entrez.read( + Entrez.esearch(db='nuccore', term=term, idtype='acc', + retstart=retstart, retmax=BATCH_SIZE) + ) + idlist = record['IdList'] + new_ids = set(idlist) + num_read = len(new_ids) + print(num_read,":",idlist[0],file=sys.stderr) + retstart += num_read + new_ids.difference_update(skip) # remove skip ids + new_ids = set([id for id in new_ids if id[:2] not in PREFIX]) + ids.update(new_ids) # add to total set + print(f"Term: {term} --> #{len(new_ids)} new IDs ---> Total unique IDs #{len(ids)})",file=sys.stderr) + if args.max and len(ids) > args.max: + print(f"Stopping past #{args.max} items",file=sys.stderr) + break + +for id in ids: + print(id) + +sys.exit(2) + +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(outdir) +for i, id_x_list in enumerate(chunks(list(id_set), num_ids_for_request)): + path_metadata_xxx_xml = os.path.join(outdir, '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() + ) |