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[BUG] IntegronFinder fails when there is a "space" in the path #99

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eloilit opened this issue Jul 25, 2022 · 1 comment
Closed
1 of 3 tasks

[BUG] IntegronFinder fails when there is a "space" in the path #99

eloilit opened this issue Jul 25, 2022 · 1 comment
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@eloilit
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eloilit commented Jul 25, 2022

Describe the bug
On a Mac, IntegronFinder bugs when there is a "space" character in the path to the genome file

To Reproduce
Steps to reproduce the behavior:

  1. Create a path with a space included (e.g. /user/Genus species/genome.fasta
  2. integron_finder --local-max genome.fasta

Expected behavior

Normal run

Please complete the following information):

OS:

  • Linux
  • Windows
  • Mac

Integron_Finder Version:

copy/paste here the output of integron_finder --version

integron_finder version 2.0.2
Using:

  • Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 17:01:00) [Clang 13.0.1 ]

  • numpy 1.19.4

  • pandas 1.1.5

  • matplolib 3.3.3

  • biopython 1.78

  • Prodigal V2.6.3: February, 2016

  • INFERNAL 1.1.4 (Dec 2020)

  • HMMER 3.3.2 (Nov 2020); http://hmmer.org/

Additional context
It's not truly important, but could be the source of a problem with people having few experience with bioinformatics
@eloilit eloilit added the bug label Jul 25, 2022
@eloilit eloilit changed the title [BUG] [BUG] IntegronFinder fails when there is a "space" in the path Jul 25, 2022
bneron added a commit that referenced this issue Jul 26, 2022
@bneron
🐛 fix issue #99 IF fails when there is a "space" in the path
30ba816 
When generated the command lines for external tools
(prodigal/hmmsearc/cmsearch) the path were not protected

instead to split by hand, use shlex.split which is smarter
better split and protect path in same time

switch also subprocess.call to subprocess.run to execute
external tools
@bneron bneron self-assigned this Jul 26, 2022
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bneron commented Jul 26, 2022

fixed with commit 5ae0c90

@bneron bneron closed this as completed Jul 26, 2022
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