From 2c6181c7eb86c0285928a434a37401d6680f9f79 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Fri, 1 Jan 2021 12:24:44 +0000 Subject: genbank-fetch-ids --- workflows/pull-data/genbank/README.md | 4 +- workflows/pull-data/genbank/genbank-fetch-ids.py | 114 +++++++++++++++++++++ workflows/pull-data/genbank/update-from-genbank.py | 114 --------------------- 3 files changed, 117 insertions(+), 115 deletions(-) create mode 100755 workflows/pull-data/genbank/genbank-fetch-ids.py delete mode 100755 workflows/pull-data/genbank/update-from-genbank.py diff --git a/workflows/pull-data/genbank/README.md b/workflows/pull-data/genbank/README.md index c235be7..f442b5d 100644 --- a/workflows/pull-data/genbank/README.md +++ b/workflows/pull-data/genbank/README.md @@ -3,8 +3,10 @@ ```sh # --- get list of IDs already in PubSeq sparql-fetch-ids > pubseq_ids.txt +# --- get list of missing genbank IDs +genbank-fetch-ids --skip pubseq_ids.txt > genbank_ids.txt # --- fetch XML -update-from-genbank.py --skip pubseq_ids.txt --outdir ~/tmp/genbank +update-from-genbank.py --ids genbank_ids.txt --outdir ~/tmp/genbank # --- Transform to YAML and FASTA transform-genbank-xml2yamlfa --dir ~/tmp/genbank id --outdir ~/tmp/pubseq ``` diff --git a/workflows/pull-data/genbank/genbank-fetch-ids.py b/workflows/pull-data/genbank/genbank-fetch-ids.py new file mode 100755 index 0000000..e62a611 --- /dev/null +++ b/workflows/pull-data/genbank/genbank-fetch-ids.py @@ -0,0 +1,114 @@ +#!/usr/bin/env python3 +# +# - bulk download genbank data and matadata, preparing the FASTA and +# the YAML files +# +# 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('--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' # FIXME + +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 # batch calls +min_acceptable_collection_date = datetime(2019, 12, 1) + +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!") + +skip = set() +if args.skip: + with open(args.skip) as f: + content = f.readlines() + for line in content: + skip.add(line.strip()) + +print(f"Skip size is {len(skip)}",file=sys.stderr) + +# ---------------------------------------------------------------------- +""" +Download section for genbank XML +""" + +# 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() + ) diff --git a/workflows/pull-data/genbank/update-from-genbank.py b/workflows/pull-data/genbank/update-from-genbank.py deleted file mode 100755 index e62a611..0000000 --- a/workflows/pull-data/genbank/update-from-genbank.py +++ /dev/null @@ -1,114 +0,0 @@ -#!/usr/bin/env python3 -# -# - bulk download genbank data and matadata, preparing the FASTA and -# the YAML files -# -# 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('--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' # FIXME - -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 # batch calls -min_acceptable_collection_date = datetime(2019, 12, 1) - -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!") - -skip = set() -if args.skip: - with open(args.skip) as f: - content = f.readlines() - for line in content: - skip.add(line.strip()) - -print(f"Skip size is {len(skip)}",file=sys.stderr) - -# ---------------------------------------------------------------------- -""" -Download section for genbank XML -""" - -# 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() - ) -- cgit v1.2.3