Custom genome installation in SigProfileMatrixGenerator

Question

[Ian]

I would be interested to hear from anyone who has added a custom genome (other than those created by the authors) to SigProfilerMatrixGenerator. https://github.com/AlexandrovLab/SigProfilerMatrixGenerator

I have been able to successfully run it with 'mm39', but have been unable to install a genome for BALB_cJ.

Chromosome information appears to be processed, but the genome installation fails at the transcript step:

Chromosome string files for BALB_cJ have been created. Continuing with installation.
[DEBUG] Chromosome tsb files found at: <MY_PATH>/.conda/envs/FreeBayes135/lib/python3.9/site-packages/SigProfilerMatrixGeneratorreferences/chromosomes/tsb/BALB_cJ/
The transcriptional reference data for BALB_cJ has not been saved. Creating these files now
Traceback (most recent call last):
File "<MY_PATH>/.conda/envs/FreeBayes135/lib/python3.9/site-packages/SigProfilerMatrixGenerator/scripts/save_tsb_192.py", line 347, in
main()
File "<MY_PATH>/.conda/envs/FreeBayes135/lib/python3.9/site-packages/SigProfilerMatrixGenerator/scripts/save_tsb_192.py", line 344, in main
save_tsb(chromosome_string_path, transcript_path, output_path)
File "<MY_PATH>/.conda/envs/FreeBayes135/lib/python3.9/site-packages/SigProfilerMatrixGenerator/scripts/save_tsb_192.py", line 85, in save_tsb
out.close()
UnboundLocalError: local variable 'out' referenced before assignment
The transcriptional reference data for BALB_cJ has been saved.
All reference files have been created.
To proceed with matrix_generation, please provide the path to your vcf files and an appropriate output path.
Installation complete.

HOWEVER: '<MY_PATH>/.conda/envs/FreeBayes135/lib/python3.9/site-packages/SigProfilerMatrixGeneratorreferences/chromosomes/tsb/BALB_cJ/' is empty.

If you could give a working example that would be helpful.

Thanks.

Answer 1

[Ian]

This problem has been fixed as of version 1.1.30.

[jnverb]

Hi Ian, just wondering how you installed your custom genome because I can't seem to find how in the documentation other than the genInstall() specifying the offline file path. Cheers!

[Ian]

The documentation doesn't seem to include the instructions for custom genomes anymore. I used the info here: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/issues/35