Created
August 21, 2019 06:56
-
-
Save rwst/760ee4454d306c4f619053bf5798becd to your computer and use it in GitHub Desktop.
creating QuickStatement batches for missing claims on Wikidata objects about genes and their corresponding OMIM entries
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
from sys import * | |
import csv | |
reader = csv.DictReader(open('gene-entrezids.tab', 'r'), delimiter='\t') | |
genes = {} | |
for item in reader: | |
gid = item.get('geneid') | |
iturl = item.get('item') | |
iturl = iturl[iturl.rfind('/')+1:] | |
gitem = genes.get(gid) | |
if gitem is not None: | |
if iturl != gitem[0]: | |
print('duplicate gene id: {} {} {}'.format(gid,gitem,iturl)) | |
continue | |
else: | |
name = item.get('itemLabel') | |
genes[gid] = (iturl, name) | |
reader = csv.DictReader(open('mim2gene.txt', 'r'), delimiter='\t') | |
mims = {} | |
for item in reader: | |
type = item.get('mtype') | |
if type != 'gene': | |
continue | |
gid = item.get('gid') | |
gene = genes.get(gid) | |
mimid = item.get('mimid') | |
name = item.get('gname') | |
if gene is None and gid is not None and len(gid) > 0: | |
print('missing gene: {} Entrez: {} OMIM: {}'.format(name,gid,mimid)) | |
if gene is None: | |
continue | |
it = gene[0] | |
na = gene[1] | |
if name != na: | |
print('name mismatch: {} ({}) {}'.format(name, gid, na)) | |
print('{}|P492|"{}"'.format(it, mimid)) | |
#print('{}|P492|"{}"|S248|Q241953|S813|+2019-08-19T00:00:00Z/11'.format(it, mimid)) |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment