From ee01616a8c5ab5449325599dfaea32341f049784 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Fri, 1 Jan 2021 15:43:47 +0000 Subject: update-from-genbank.py --- workflows/pull-data/genbank/README.md | 2 +- workflows/pull-data/genbank/genbank-fetch-ids | 5 -- workflows/pull-data/genbank/genbank-fetch-ids.py | 69 ++++------------------ workflows/pull-data/genbank/update-from-genbank.py | 43 ++++++++++++++ 4 files changed, 56 insertions(+), 63 deletions(-) delete mode 100755 workflows/pull-data/genbank/genbank-fetch-ids create mode 100755 workflows/pull-data/genbank/update-from-genbank.py (limited to 'workflows/pull-data') diff --git a/workflows/pull-data/genbank/README.md b/workflows/pull-data/genbank/README.md index d7c294b..479ddc9 100644 --- a/workflows/pull-data/genbank/README.md +++ b/workflows/pull-data/genbank/README.md @@ -6,7 +6,7 @@ sparql-fetch-ids > pubseq_ids.txt # --- get list of missing genbank IDs genbank-fetch-ids.py --skip pubseq_ids.txt > genbank_ids.txt # --- fetch XML -update-from-genbank.py --ids genbank_ids.txt --outdir ~/tmp/genbank +update-from-genbank.py --ids genbank_ids.txt --out ~/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 b/workflows/pull-data/genbank/genbank-fetch-ids deleted file mode 100755 index 24fe4c7..0000000 --- a/workflows/pull-data/genbank/genbank-fetch-ids +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/sh -# -# genbank-fetch-ids > genbank_ids.tx - -curl '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' diff --git a/workflows/pull-data/genbank/genbank-fetch-ids.py b/workflows/pull-data/genbank/genbank-fetch-ids.py index e62a611..1962daa 100755 --- a/workflows/pull-data/genbank/genbank-fetch-ids.py +++ b/workflows/pull-data/genbank/genbank-fetch-ids.py @@ -1,46 +1,33 @@ #!/usr/bin/env python3 # -# - bulk download genbank data and matadata, preparing the FASTA and -# the YAML files +# Find all genbank IDs # -# update-from-genbank.py --max 10 --skip ids.txt --outdir ~/tmp/genbank +# genbank-fetch-ids.py --max 1000 --skip pubseq_ids.txt # -# See directory .guix-run and README.md +# See also 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 - +import sys +import xml.etree.ElementTree as ET 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 +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) +args = parser.parse_args() -num_ids_for_request = 100 # batch calls -min_acceptable_collection_date = datetime(2019, 12, 1) +from Bio import Entrez +Entrez.email = 'another_email@gmail.com' # FIXME -outdir = args.outdir +# min_acceptable_collection_date = datetime(2019, 12, 1) 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: @@ -51,11 +38,6 @@ if args.skip: 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 @@ -85,30 +67,3 @@ for term in TERMS: 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 new file mode 100755 index 0000000..6d6d90c --- /dev/null +++ b/workflows/pull-data/genbank/update-from-genbank.py @@ -0,0 +1,43 @@ +#!/usr/bin/env python3 +# +# bulk download genbank data and matadata, preparing the FASTA and the +# YAML files +# +# update-from-genbank.py --max 10 --ids ids.txt --out ~/tmp/genbank-xml +# +# See also directory .guix-run and README.md + +import argparse +import os +import sys +from utils import chunks + +from Bio import Entrez +Entrez.email = 'another_email@gmail.com' # FIXME + +BATCH=100 + +parser = argparse.ArgumentParser() +parser.add_argument('--max', type=int, help='Max queries', required=False) +parser.add_argument('--ids', type=str, help='File with ids to fetch, 1 id per line', required=True) +parser.add_argument('--out', type=str, help='Directory to write to', required=True) +args = parser.parse_args() + +ids = set() +with open(args.ids) as f: + content = f.readlines() + for line in content: + ids.add(line.strip()) + +dir = args.out +if not os.path.exists(dir): + raise Exception(f"Directory {dir} does not exist") + +request_num = min(BATCH,args.max) +for i, idsx in enumerate(chunks(list(ids), request_num)): + xmlfn = os.path.join(dir, f"metadata_{i}.xml") + print(f"Fetching {xmlfn} ({i*request_num})",file=sys.stderr) + with open(xmlfn, 'w') as f: + f.write(Entrez.efetch(db='nuccore', id=idsx, retmode='xml').read()) + if i*request_num >= args.max: + break -- cgit v1.2.3