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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, "$locus_name.tfa")" it works correctly again.
If this modification is correct, could you please update the mentalist code ?
Best regards,
HPhilippon
The text was updated successfully, but these errors were encountered:
Hi,
I have tested MentaList on August 2020 and MLST profiles were correctly downloaded using the following command lines for exemple:
conda create -n mentalist
conda activate mentalist
conda install -c bioconda -c conda-forge mentalist
mentalist download_pubmlst -k 31 -o Ecoli_schemes -s 53 --db E_colie_1.db
But in September this does not work anymore because, I think, pubmlst.org has changed the fasta profile files names (all adk.tfa, fumC.tfa, gyrB.tfa, etc. are now named "sequence_fasta"). The downloaded files are then overwritten.
By modifying the line 96 of the "mlst_download_functions.jl" file from "filepath = _download_to_folder(locus_url, output_dir)" to "filepath = _download_to_folder(locus_url, output_dir, false, "$locus_name.tfa")" it works correctly again.
If this modification is correct, could you please update the mentalist code ?
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
The text was updated successfully, but these errors were encountered: