Add Klebsiella pneumoniae ptf

[ryanjameskennedy]

I noticed that this repository doesn't have a prodigal training file for Klebsiella pneumonia which has clinical importance to our hospital and our pipeline uses this repository as a submodule (JASEN if you're interested). I ran the following command on NC_016845.1:

prodigal -i <reference>.fna -t <output_training_file>.trn -p single

I hope that's okay that I'm creating a PR for this:)

[rfm-targa]

Hello @ryanjameskennedy,

Thank you for your interest in chewBBACA. I noticed that you used the Nucleotide record NC_016845.1 to create the training file, but in the line added to the list of available training files it points to the Assembly record GCF_000240185.1. We usually create the training files based on the Assembly records. Is there any reason you created the training file based on the Nucleotide record and not the Assembly record?

Kind regards,

Rafael

[rfm-targa]

Also, we are working on the release of version 3.3.0. It includes new features and several bug fixes. It should be released soon. Just letting you know in case you're using chewBBACA v3 in JASEN and want to update to get the latest features and a slight improvement in accuracy for some particular cases.

[ryanjameskennedy]

When I initially created the PR it was for a prodigal training file repository that had used nucleotide files instead of assemblies. I will rerun this and push the changes! I will update to 3.3.0 when it's available:)

[ryanjameskennedy]

I have rerun prodigal using the assembly record (GCF_000240185.1) as follows:

prodigal -i GCF_000240185.1_ASM24018v2_genomic.fna -t Klebsiella_pneumoniae.trn -p single

[rfm-targa]

Hello @ryanjameskennedy,

Thank you for updating the training file. I will approve the PR. Thank you for contributing!

Best regards,

Rafael