Can't use -m parameter

[Wesady]

HI When I use command like openrdp -c test_cfg.ini -m geneconv -o ***.csv ***.fasta, there's an error: openrdp: error: argument -m/--methods: invalid choice: '[geneconv]' (choose from 'geneconv', 'bootscan', 'maxchi', 'siscan', 'chimaera', 'threeseq', 'rdp'). I can't find any help from document. Can you help me? THANK YOU!

[WilliamZekaiWang]

Hi,

I tried to replicate your issue with the the same test_cfg.ini file and other arguments you provided in that order and it worked on my end through the latest version of the master branch with the python/dependency versions specified in the readme.

I did see a similar error when I put the command without specifying output and config file:

/OpenRDP# openrdp -m genecov test.fasta
usage: openrdp [-h] [-r REF] [-o OUTFILE] [-c CFG] [-m  [...]] [-q] infile
openrdp: error: argument -m/--methods: invalid choice: 'genecov' (choose from 'geneconv', 'bootscan', 'maxchi', 'siscan', 'chimaera', 'threeseq', 'rdp')

For some reason, putting -q after -m genecov and specifying the config file fixed this issue for me. Perhaps it could be a temporary fix for you as well? i.e.: openrdp -c test_config.ini -m genecov -q test.fasta

Could you also provide more information regarding the python version you are using?

[Wesady]

Add -q worked, THANK YOU VERY MUCH!

[ArtPoon]

Something's weird about this - that should not have worked because there's a typo in genecov Running master branch, commit 1d1c29969c5382f3c249ad221c8bee9f9e0bcab8, I cannot reproduce this issue:

(venv) art@orolo:~/git/OpenRDP$ openrdp -c tests/test_cfg.ini -m geneconv -o atest.csv tests/CRF_07_test.fasta 
Loading configuration from tests/test_cfg.ini
Starting GENECONV Analysis
Finished GENECONV Analysis
Scanning triplet 1 / 1

Method      Start   End Recombinant Parent1 Parent2 Pvalue
------------------------------------------------------------------------
Geneconv    8972    9114    B           07_BC   -       0.00E+00
Geneconv    4416    5139    C           07_BC   -       1.17E-03
Geneconv    5927    5957    B           07_BC   -       9.04E-03
Geneconv    8219    8322    C           07_BC   -       3.10E-02
Geneconv    8972    9118    C           -       -       0.00E+00
Geneconv    2193    2365    C           -       -       1.70E-04
Geneconv    4416    5139    B           -       -       7.58E-03
Geneconv    5700    5771    C           -       -       1.92E-02
Geneconv    1   1229    B           -       -       2.10E-02
Geneconv    5927    5957    C           -       -       6.17E-02

[ArtPoon]

@Wesady can you please provide the following information:

• your operating system
• version of Python
• version of OpenRDP My guess is that you are running an older version of argparse that handles single choice inputs differently

[Wesady]

Yeah, but what I used is geneconv. And my operating system is Ubuntu 20.04.6 LTS, version of Python is 3.9.18, version of OpenRDP was cloned from this repository on Feb 2nd.

[ArtPoon]

Closing with a no repro