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Documentation improvement #24

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Bio-finder opened this issue Feb 13, 2023 · 0 comments
Open

Documentation improvement #24

Bio-finder opened this issue Feb 13, 2023 · 0 comments
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documentation Improvements or additions to documentation

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@Bio-finder
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Hello,
I have been working with your tool and noticed that something was not very clear in the doc: the ISOLATE name in the mdu qc file MUST be the same as in the matches from the run => the prefix of the output directory or the program crashes with the following error:

Traceback (most recent call last): File "/usr/local/bin/lmod/abritamr/1.0.13/bin/abritamr", line 10, in <module> sys.exit(main()) ^^^^^^ File "/usr/local/bin/lmod/abritamr/1.0.13/lib/python3.11/site-packages/abritamr/abritamr.py", line 129, in main args.func(args) File "/usr/local/bin/lmod/abritamr/1.0.13/lib/python3.11/site-packages/abritamr/abritamr.py", line 28, in mdu C.run() File "/usr/local/bin/lmod/abritamr/1.0.13/lib/python3.11/site-packages/abritamr/Collate.py", line 822, in run passed_match_df = self.mdu_reporting_general(match=self.match) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/bin/lmod/abritamr/1.0.13/lib/python3.11/site-packages/abritamr/Collate.py", line 769, in mdu_reporting_general exp_species = qcdf["SPECIES_EXP"].values[0] ~~~~~~~~~~~~~~~~~~~~~~~~~~^^^ IndexError: index 0 is out of bounds for axis 0 with size 0

I would thus process this error in a more meaningful one in the code or specify it a bit more clearly when you speak about the qc file.
Best regards,

@kristyhoran kristyhoran self-assigned this Feb 29, 2024
@kristyhoran kristyhoran added the documentation Improvements or additions to documentation label Feb 29, 2024
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