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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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ambiguous error message #38

Closed anna-panchenko closed 4 years ago

anna-panchenko commented 4 years ago

Specifying a wrong format type (VCF, not MAF) produces an uninformative message:

(env_mutagene) Annas-MBP:mutagene panch$ mutagene signature identify -i data_mutations_extended.txt -g hg19 -s 49 -U -b -f VCF Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/runpy.py", line 193, in _run_module_as_main "main", mod_spec) File "/Library/Frameworks/Python.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/signature_menu.py", line 117, in callback self.identify(args) File "/Users/panch/mutagene/env_mutagene/lib/python3.7/site-packages/mutagene/cli/signature_menu.py", line 94, in identify mutations, processing_stats = read_auto_profile(args.infile, fmt=args.input_format, asm=args.genome) File "/Users/panch/mutagene/env_mutagene/lib/python3.7/site-packages/mutagene/io/mutations_profile.py", line 115, in read_auto_profile mutations, processing_stats = read_VCF_profile(mutations_lines, asm) File "/Users/panch/mutagene/env_mutagene/lib/python3.7/site-packages/mutagene/io/mutations_profile.py", line 234, in read_VCF_profile pos = int(col_list[1]) # VCF POS ValueError: invalid literal for int() with base 10: 'Entrez_Gene_Id'

neksa commented 4 years ago

It's a Python exception.

Are you trying to process MAF file as a VCF?

anna-panchenko commented 4 years ago

yes

On Thu, Apr 9, 2020 at 7:52 PM Alexander Goncearenco < notifications@github.com> wrote:

It's a Python exception.

Are you trying to process MAF file as a VCF?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/neksa/mutagene/issues/38#issuecomment-611807145, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADBVIIYSVBGMH4LOMAL35HDRLZNUTANCNFSM4MFCSTIQ .

anna-panchenko commented 4 years ago

the users will not always know which format they are using

On Thu, Apr 9, 2020 at 7:52 PM Alexander Goncearenco < notifications@github.com> wrote:

It's a Python exception.

Are you trying to process MAF file as a VCF?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/neksa/mutagene/issues/38#issuecomment-611807145, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADBVIIYSVBGMH4LOMAL35HDRLZNUTANCNFSM4MFCSTIQ .