'name2' keyError

[Walter Eckalbar]

Hi devs! I’m trying to get your software working for automation of picking large amounts of sgRNAs for some screens, but am encountering the following error:

Traceback (most recent call last):
  File "/home/walter/tools/valenlab-chopchop-a4359cbe255a/chopchop.py", line 3304, in <module>
    main()
  File "/home/walter/tools/valenlab-chopchop-a4359cbe255a/chopchop.py", line 2865, in main
    args.outputDir, args.consensusUnion, args.jsonVisualize, args.guideSize)
  File "/home/walter/tools/valenlab-chopchop-a4359cbe255a/chopchop.py", line 2278, in parseTargets
    gene, txInfo = geneToCoord_file(target_string, data)
  File "/home/walter/tools/valenlab-chopchop-a4359cbe255a/chopchop.py", line 1107, in geneToCoord_file
    if row['name'] == gene_in or row['name2'] == gene_in or row['name'] == gene_in.upper() \
KeyError: 'name2'

‌

I am not sure if you are actively maintaining this or not, as it is still on python2, but suggestions would be appreciated. Thanks.

[Qian Yu]

Hi,

I have met the same error. I think the problem is that the refFlat gene_table doesn’t contain ‘name2' column.

So I went to UCSC table browser, and I downloaded ‘UCSC RefSeq(refGene)’ instead of ‘refFlat’. Then the script work again for me!

Best.

[Kornel Labun]

added to the documentation in README