sanger-pathogens / ariba

Antimicrobial Resistance Identification By Assembly
http://sanger-pathogens.github.io/ariba/
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Ignore comments column and drop Bio.Alphabet #319

Closed rpetit3 closed 2 years ago

rpetit3 commented 2 years ago

The MLST profile for Candida glabrata has a column named comments which is not in the ignore list. This PR adds it to the ignore list, as well as drops Bio.Alphabet which has been removed in latest Biopython versions.

https://pubmlst.org/bigsdb?db=pubmlst_cglabrata_seqdef&page=downloadProfiles&scheme_id=1

ST  FKS LEU2    NMT1    TRP1    UGP1    URA3    comments
1   7   1   1   6   4   4   
2   1   2   2   1   1   1   
3   5   7   8   7   3   6   
4   7   3   9   8   1   5   
5   5   7   8   1   3   6   
6   2   5   7   5   1   2   
7   3   4   4   3   3   4   
8   1   2   2   1   2   1   
puethe commented 2 years ago

Thanks!