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bvalot / pyMLST

whole genome MLST analysis
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multi-fasta file for scheme creation #3

Closed 215220606 closed 2 years ago

215220606 commented 2 years ago

Hi,

Instead of downloading the scheme from https://www.cgmlst.org/ I want to create one with a downloaded external file from a Core genome analysis in publication with the wgMLST create option.

I wonder how the multi-fasta file containing sequences of genes format, specifically the alleles id, should be. It seems that a multiFasta with all the allellic variants of each loci of a specific Species do not work.

Thanks

bvalot commented 2 years ago

Hi ClaraVIS,

You need a fasta file with the genes to create a custom schema for whole genome analysis. >geneA ATGGATGCTAGT... >geneB ATGCGTCATGCTA...

But pyMLST don't use allelic variant for each genes, so the files must contains only one allele for each genes.

215220606 commented 2 years ago

Hello bvalot,

Thank you very much. It worked with one allele per gene.

:)

bvalot commented 2 years ago

OK good.