KeyError from pyfaidx can mean that the chromosome labels in the ref fasta and vcf don't match

[TeresaPegan]

Hi, I got this error and I figured it out, but I thought I would post this here because it requires a close look at the scripts to figure out how to interpret the error. As a low-priority suggestion, it might be worth adding a more user-friendly error for this situation.

Here is the error I initially got:

Traceback (most recent call last):
  File "/Users/teresapegan/opt/miniconda3/envs/helmsman/lib/python3.6/site-packages/pyfaidx/__init__.py", line 997, in __getitem__
    return self.records[rname]
KeyError: '1'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "helmsman/helmsman.py", line 413, in <module>
    main()
  File "helmsman/helmsman.py", line 329, in main
    data_in = util.processInput(args.mode, args, subtypes_dict)
  File "/Users/teresapegan/helmsman/util.py", line 283, in __init__
    self.data = self.process_vcf(args.input)
  File "/Users/teresapegan/helmsman/util.py", line 400, in process_vcf
    sequence = fasta_reader[row_chr]
  File "/Users/teresapegan/opt/miniconda3/envs/helmsman/lib/python3.6/site-packages/pyfaidx/__init__.py", line 999, in __getitem__
    raise KeyError("{0} not in {1}.".format(rname, self.filename))
KeyError: '1 not in MutSpect/Spalm_arbitrary_reference.fasta.'

It turns out this was simply because my VCF had a chromosome label of "1" and my reference fasta had a more complex chromosome label with species name in it. When I changed the reference fasta chromosome label, then helmsman worked.

Hope this is helpful, -Teresa