mentalist download_pubmlst does not download the expected files

[axbazin]

Hello,

When trying the example in the doc:
mentalist download_pubmlst -k 31 -o campy_mlst_fasta_files -s 28 --db campy_mlst.db
I get the following log:

INFO: Searching for the scheme ...
2022-10-12T09:23:48.936 - info: Downloading scheme for Campylobacter helveticus ...
2022-10-12T09:23:49.233 - info: Downloading profile ...
Trying to download: https://rest.pubmlst.org/db/pubmlst_campylobacter_nonjejuni_seqdef/schemes/1/profiles_csv
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   234    0   234    0     0    507      0 --:--:-- --:--:-- --:--:--   951
2022-10-12T09:23:49.917 - info: Downloading locus Che_aspA ...
Trying to download: https://rest.pubmlst.org/db/pubmlst_campylobacter_nonjejuni_seqdef/loci/Che_aspA/alleles_fasta
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  3430    0  3430    0     0  17290      0 --:--:-- --:--:-- --:--:-- 17411
2022-10-12T09:23:50.129 - info: Downloading locus Che_atpA ...
Trying to download: https://rest.pubmlst.org/db/pubmlst_campylobacter_nonjejuni_seqdef/loci/Che_atpA/alleles_fasta
2022-10-12T09:23:50.13 - info: Downloading locus Che_glnA ...
Trying to download: https://rest.pubmlst.org/db/pubmlst_campylobacter_nonjejuni_seqdef/loci/Che_glnA/alleles_fasta
2022-10-12T09:23:50.13 - info: Downloading locus Che_gltA ...
Trying to download: https://rest.pubmlst.org/db/pubmlst_campylobacter_nonjejuni_seqdef/loci/Che_gltA/alleles_fasta
2022-10-12T09:23:50.13 - info: Downloading locus Che_glyA ...
Trying to download: https://rest.pubmlst.org/db/pubmlst_campylobacter_nonjejuni_seqdef/loci/Che_glyA/alleles_fasta
2022-10-12T09:23:50.13 - info: Downloading locus Che_pgm ...
Trying to download: https://rest.pubmlst.org/db/pubmlst_campylobacter_nonjejuni_seqdef/loci/Che_pgm/alleles_fasta
2022-10-12T09:23:50.13 - info: Downloading locus Che_tkt ...
Trying to download: https://rest.pubmlst.org/db/pubmlst_campylobacter_nonjejuni_seqdef/loci/Che_tkt/alleles_fasta
2022-10-12T09:23:50.131 - info: Finished downloading.
2022-10-12T09:23:50.138 - info: Building the k-mer database ...
2022-10-12T09:23:50.415 - info: Opening FASTA files ...
2022-10-12T09:23:55.517 - info: Combining results for each locus ...
2022-10-12T09:23:55.678 - info: Saving DB ...
2022-10-12T09:23:57.339 - info: Done!

and when looking at the content of 'campy_mlst_fasta_files':

$ ls campy_mlst_fasta_files

alleles_fasta  profiles_csv

I did not notice at first, so I executed mentalist on those files and got super weird outputs like this (example from an E.coli db downloaded the same way than above) :
mentalist call -o wgMLST.txt --db Escherichia_coli.db --fasta -1 Ecoli.CDS.fna

cat wgMLST.txt
Sample  alleles_fasta   alleles_fasta   alleles_fasta   alleles_fasta   alleles_fasta   alleles_fasta   alleles_fasta   ST      clonal_complex
Ecoli.CDS.fna   0       0       0       0       0       0       53      0       0

Mentalist was installed from bioconda, using version 0.2.4.

Did an update from pubmlst break the tool, or am I doing something wrong?

Adelme

[axbazin]

Hi @pedrofeijao, since this was fixed by pull request #129, is there a chance you could do a release so that the conda recipe gets updated and we can install the fixed version with conda?