MLST profile no more downloaded from pubmlst

[Hphilippon]

Hi,
I have tested MentaList on August 2020 and MLST profiles were correctly downloaded using the following command lines for exemple:
conda create -n mentalist
conda activate mentalist
conda install -c bioconda -c conda-forge mentalist
mentalist download_pubmlst -k 31 -o Ecoli_schemes -s 53 --db E_colie_1.db

But in September this does not work anymore because, I think, pubmlst.org has changed the fasta profile files names (all adk.tfa, fumC.tfa, gyrB.tfa, etc. are now named "sequence_fasta"). The downloaded files are then overwritten.

By modifying the line 96 of the "mlst_download_functions.jl" file from "filepath = _download_to_folder(locus_url, output_dir)" to "filepath = _download_to_folder(locus_url, output_dir, false, "$locus_name.tfa")" it works correctly again.
If this modification is correct, could you please update the mentalist code ?

Best regards,

HPhilippon

[slvrshot]

Hi,
I have tested MentaList on August 2020 and MLST profiles were correctly downloaded using the following command lines for exemple:
conda create -n mentalist
conda activate mentalist
conda install -c bioconda -c conda-forge mentalist
mentalist download_pubmlst -k 31 -o Ecoli_schemes -s 53 --db E_colie_1.db

But in September this does not work anymore because, I think, pubmlst.org has changed the fasta profile files names (all adk.tfa, fumC.tfa, gyrB.tfa, etc. are now named "sequence_fasta"). The downloaded files are then overwritten.

By modifying the line 96 of the "mlst_download_functions.jl" file from "filepath = _download_to_folder(locus_url, output_dir)" to "filepath = _download_to_folder(locus_url, output_dir, false, "$locus_name.tfa")" it works correctly again.
If this modification is correct, could you please update the mentalist code ?

Best regards,

HPhilippon

Do you have a fork of this for conda install? thx