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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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motif search #33

Closed anna-panchenko closed 4 years ago

anna-panchenko commented 4 years ago

It is not clear which motif is used by default. If "--motif" argument is missing, the program is hanging for long time and then returns an error. It should return a warning: "motif is not specified" in the beginning.

mutagene motif -i sample.maf

Traceback (most recent call last): File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.4/lib/python3.7/runpy.py", line 193, in _run_module_as_main "main", mod_spec) File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.4/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/global/home/hpc4498/venv/lib/python3.7/site-packages/mutagene/main.py", line 113, in MutaGeneApp() File "/global/home/hpc4498/venv/lib/python3.7/site-packages/mutagene/main.py", line 104, in init parser_class.callback(args) File "/global/home/hpc4498/venv/lib/python3.7/site-packages/mutagene/cli/motif_menu.py", line 149, in callback MotifMenu.search(args) File "/global/home/hpc4498/venv/lib/python3.7/site-packages/mutagene/cli/motif_menu.py", line 127, in search dump_matches=args.save_motif_matches) if mutations_with_context is not None else [] File "/global/home/hpc4498/venv/lib/python3.7/site-packages/mutagene/motifs/init.py", line 46, in identify_motifs motifs = get_known_motifs() File "/global/home/hpc4498/venv/lib/python3.7/site-packages/mutagene/io/motifs.py", line 21, in get_known_motifs with open(fname, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/global/home/hpc4498/venv/lib/python3.7/site-packages/mutagene/io/../data/motifs/motifs.json' (venv) [hpc4498@caclogin02 mutagene]$ (venv) [hpc4498@caclogin02 mutagene]$ mutagene motif -i TCGA.COAD.mutect.somatic.maf -w 250 -t 0.1 -o tmp1 -g hg38 Traceback (most recent call last): File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.4/lib/python3.7/runpy.py", line 193, in _run_module_as_main "main", mod_spec) File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.4/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/global/home/hpc4498/venv/lib/python3.7/site-packages/mutagene/main.py", line 113, in MutaGeneApp() File "/global/home/hpc4498/venv/lib/python3.7/site-packages/mutagene/main.py", line 104, in init parser_class.callback(args) File "/global/home/hpc4498/venv/lib/python3.7/site-packages/mutagene/cli/motif_menu.py", line 149, in callback MotifMenu.search(args) File "/global/home/hpc4498/venv/lib/python3.7/site-packages/mutagene/cli/motif_menu.py", line 127, in search dump_matches=args.save_motif_matches) if mutations_with_context is not None else [] File "/global/home/hpc4498/venv/lib/python3.7/site-packages/mutagene/motifs/init.py", line 46, in identify_motifs motifs = get_known_motifs() File "/global/home/hpc4498/venv/lib/python3.7/site-packages/mutagene/io/motifs.py", line 21, in get_known_motifs with open(fname, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/global/home/hpc4498/venv/lib/python3.7/site-packages/mutagene/io/../data/motifs/motifs.json'

neksa commented 4 years ago

It was a packaging error. Please update to 0.9.0.1 By default it will search for all known motifs.