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/update-from-genbank.py | 114 ---------------------
 1 file changed, 114 deletions(-)
 delete mode 100755 workflows/pull-data/genbank/update-from-genbank.py

(limited to 'workflows/pull-data/genbank/update-from-genbank.py')

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()
-        )
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