genbank-fetch-ids

1 files changed, 114 insertions, 0 deletions

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()
+        )