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MorrellLAB / BAD_Mutations

Deleterious mutation prediction pipeline
MIT License
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Bad fasta parse #16

Closed fayjustin closed 8 years ago

fayjustin commented 8 years ago

Using the command: python BAD_Mutations.py -v DEBUG \ predict \ --config BAD_Mutations_Config.txt \ --alignment test1/test_MSA.fasta \ --tree test1/test.tree \ --substitutions subs.txt

gives an error: Traceback (most recent call last): File "BAD_Mutations.py", line 327, in main() File "BAD_Mutations.py", line 266, in main arguments_valid, msg = parse_args.validate_args(config_opts, loglevel) File "/media/jfay/data1/projects/barley/BAD_Mutations/lrt_predict/General/parse_args.py", line 359, in validate_args if not parse_input.valid_fasta(args['fasta'], log): KeyError: 'fasta'

I think fasta should be alignment, however, that change gave me an error that the input fasta file is not valid.

Tom, I'll send you fasta alignment and tree file by email so you can reproduce.

TomJKono commented 8 years ago

Fixed argument handling and fasta/alignment/tree parsing in 1d814291ac1adc510cb4cc671a666c24986e6579