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.
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.