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MorrellLAB / BAD_Mutations

Deleterious mutation prediction pipeline
MIT License
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Compile Bug - Won't work on test data #52

Open conJUSTover opened 4 years ago

conJUSTover commented 4 years ago

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 commented 4 years ago

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

TomJKono commented 4 years ago

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 commented 4 years ago

Perfect, thanks so much!

TomJKono commented 4 years ago

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 commented 3 years ago

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.