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/genbank-fetch-ids.py | 69 +++++-------------------
 1 file changed, 12 insertions(+), 57 deletions(-)

(limited to 'workflows/pull-data/genbank/genbank-fetch-ids.py')

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()
-        )
-- 
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