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neksa / mutagene

Python library and package for mutational analysis
https://www.ncbi.nlm.nih.gov/projects/mutagene/
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Ranking, can not override profile #56

Closed anna-panchenko closed 3 years ago

anna-panchenko commented 3 years ago

$ mutagene -v rank -g hg38 -i TCGA.COAD.mutect.somatic.maf --profile TCGA.COAD.mutect.somatic.maf INFO Loaded 230248 mutations INFO Loaded 190240 protein mutations in 399 samples skipped 74543 protein mutations INFO Cohort size: 399 INFO Profile overridden INFO THRESHOLD_DRIVER: 8.030647e-05 INFO THRESHOLD_PASSENGER: 0.003440945 Traceback (most recent call last): File "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.7/lib/python3.7/runpy.py", line 193, in _run_module_as_main "main", mod_spec) File "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.7/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/Users/panch/mutagene/env_mutagene/lib/python3.7/site-packages/mutagene/main.py", line 113, in MutaGeneApp() File "/Users/panch/mutagene/env_mutagene/lib/python3.7/site-packages/mutagene/main.py", line 104, in init parser_class.callback(args) File "/Users/panch/mutagene/env_mutagene/lib/python3.7/site-packages/mutagene/cli/rank_menu.py", line 114, in callback rank(protein_mutations, args.outfile, profile, cohort_aa_mutations, cohort_size, args.threshold_driver, args.threshold_passenger) File "/Users/panch/mutagene/env_mutagene/lib/python3.7/site-packages/mutagene/mutability/mutability.py", line 138, in rank mutation_model = calculate_base_substitution_mutability(profile, cohort_size) File "/Users/panch/mutagene/env_mutagene/lib/python3.7/site-packages/mutagene/mutability/mutability.py", line 111, in calculate_base_substitution_mutability assert len(counts_profile) == 96 AssertionError

neksa commented 3 years ago

if -i TCGA.COAD.mutect.somatic.maf is supplied, profile will be calculated from that MAF file, profile override is not necessary.

In order to override profile you would need the profile itself in "profile" format:

mutagene profile -g hg38 -i TCGA.COAD.mutect.somatic.maf -o COAD.profile

Once it's ready we can use the profile file

mutagene profile -g hg38 -i TCGA.COAD.mutect.somatic.maf -o COAD.profile
shandy79 commented 3 years ago

Suggested fix is to catch the error and display a meaningful error message reminding users of the profile subcommand.

shandy79 commented 3 years ago

Closed w/PR 57