neksa
commented
3 years ago Yeah It’s definitely a bug with pentanucleotide counting. Weird because it has to be a defaultdict() and that it only occurs for some or the samples. What’s the input file?
Best, Alex
On Feb 3, 2021, at 10:48 PM, yunhuip notifications@github.com wrote: I performed ranking for about 100 MAF files but had the following Key errors for several of them. Do you have any ideas about this error? Thanks!
mutagene rank -i maf -g hg38 -o ranking.txt -p sample.profile
Traceback (most recent call last): File "/usr/local/Anaconda/envs/py3.7/lib/python3.7/runpy.py", line 193, in _run_module_as_main "main", mod_spec) File "/usr/local/Anaconda/envs/py3.7/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/pengy10/.local/lib/python3.7/site-packages/mutagene/main.py", line 113, in MutaGeneApp() File "/home/pengy10/.local/lib/python3.7/site-packages/mutagene/main.py", line 104, in init parser_class.callback(args) File "/home/pengy10/.local/lib/python3.7/site-packages/mutagene/cli/rank_menu.py", line 75, in callback protein_mutations, processing_stats = read_protein_mutations_MAF(args.infile, args.genome) File "/home/pengy10/.local/lib/python3.7/site-packages/mutagene/io/protein_mutations_MAF.py", line 239, in read_protein_mutations_MAF flat_mutations[(gene, protein_mutation)]['seq5'][props['seq5']] += 1 KeyError: 'GCTGA'
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yunhuip
I performed ranking for about 100 MAF files but had the following Key errors for several of them. Do you have any ideas about this error? Thanks!
mutagene rank -i maf -g hg38 -o ranking.txt -p sample.profile
Traceback (most recent call last):
MutaGeneApp()
File "/home/pengy10/.local/lib/python3.7/site-packages/mutagene/main.py", line 104, in init
parser_class.callback(args)
File "/home/pengy10/.local/lib/python3.7/site-packages/mutagene/cli/rank_menu.py", line 75, in callback
protein_mutations, processing_stats = read_protein_mutations_MAF(args.infile, args.genome)
File "/home/pengy10/.local/lib/python3.7/site-packages/mutagene/io/protein_mutations_MAF.py", line 239, in read_protein_mutations_MAF
flat_mutations[(gene, protein_mutation)]['seq5'][props['seq5']] += 1
KeyError: 'GCTGA'
File "/usr/local/Anaconda/envs/py3.7/lib/python3.7/runpy.py", line 193, in _run_module_as_main "main", mod_spec) File "/usr/local/Anaconda/envs/py3.7/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/pengy10/.local/lib/python3.7/site-packages/mutagene/main.py", line 113, in