Compile Bug - Won't work on test data

[conJUSTover]

Hello, thanks for writing this great program! I have downloaded the newest code and working through the test data provided. Everything has worked well, until I got to the compile function. This is the command I am using:

./BAD_Mutations.py -v DEBUG compile -P Predictions_Dir -S Test_Data/CBF3.subs 2> Compile.log

And I've attached the resulting DEBUG report.
Compile.txt

I'm not sure what the source of this error is, but is -S command is not described in the manual, so I'm not sure if I'm using this correctly. The help page says it should be in the same format as the -s substitutions file, so I just used that file.

Thanks for looking into this! Hopefully it's a quick, easy fix.

[conJUSTover]

Compile.log
My apologies, here is the correct DEBUG log file

[TomJKono]

Hello,

Thank you for your patience! It looks like this might not be a bug in the compile routine, but an error in our test data! We recently made some modifications to the routine such that the compile routine expects a substitutions file that has four columns:

1. Transcript ID
2. Amino acid position of variant
3. "Alternate" (non-reference) amino acid
4. SNP ID

Additionally, you might have a slightly old version of BAD_Mutations - if you run git pull then git checkout dev from inside of the directory where you cloned it, you should get the latest routines. I will update the test dataset and let you know when it is correct, though! Thank you!

[conJUSTover]

Perfect, thanks so much!

[TomJKono]

Hello,

Thank you for your patience! I updated the test data in the package with some snippets of a recently processed barley data set. The changes are in the dev branch, and they should include the necessary input files to start a BAD_Mutations run and some sample files that should work with the compile command.

[sunshichao0916]

Hello Justin,

When I execute the compile command, I got the same log file (compile.txt), and there is no result output. This is the command I am using:
./BAD_Mutations.py -v DEBUG compile -S Test_Data/XXXX.subs -P Predictions_Dir 2> Compile.log

And I've attached the resulting DEBUG report.

Compile.log

What changes did you make at that time to get the correct result file.

I hope you can give me your advice. Thank you very much.