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AlexandrovLab / SigProfilerExtractorR

An R wrapper for SigProfilerExtractor that allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
BSD 2-Clause "Simplified" License
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cosmic v2 #16

Open ab08028 opened 5 days ago

ab08028 commented 5 days ago

Hi there, just wanted to let you know what when trying to run sigprofilerextractorR using cosmic v2, the reference file is not found: /opt/anaconda3/lib/python3.8/site-packages/SigProfilerAssignment/data/ReferenceSignatures/GRCh37/COSMICv2.0_SBS_GRCh37.txt

because that file is actually named "COSMIC_v2_SBS_GRCh37.txt"

Renaming that file to be "v2.0" instead of "v2" made the program run as expected

I imagine this would also be a problem for the "v1" labeled files too

Cheers, ~ Annabel

marcos-diazg commented 5 days ago

Dear Annabel,

Thanks so much for your feedback! Could you please let us know the exact commands you run to get this error? That would be helpful to understand a bit better where this is coming from and if this is specific only to the R implementation.

Thanks in advance. Best,

Marcos

ab08028 commented 5 days ago

Absolutely! I'm using version 1.1.16 of SigProfilerExtractorR and the command was:

sigprofilerextractor(input_type = "table", paste0(spe_outdir,"perFamily/"), input_data=paste0(inputdir,"AllSpectra.FormattedForSigProfilerExtractor.PERFAMILY.txt"), reference_genome="GRCh38", minimum_signatures=1, maximum_signatures=3, nmf_replicates=100, cosmic_version = 2)

and the error was: /opt/anaconda3/lib/python3.8/site-packages/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v2.0_SBS_GRCh37.txt file not found.

It looks like there's also a slight incompatibility that I'm specifying GRCh38 as the reference genome, but 37 is being called (I'm guessing that's the only one available for COSMIC v2?)

Thanks so much for looking into it! :)