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Russel88 / CRISPRCasTyper

CCTyper: Automatic detection and subtyping of CRISPR-Cas operons
https://typer.crispr.dk
MIT License
89 stars 16 forks source link

Execution against protein fasta and gff #33

Open xvtyzn opened 1 year ago

xvtyzn commented 1 year ago

Hi,

First of all, I would like to thank you for developing this wonderful tool.

My question is about the input files of the tool. Currently I have a genome sequence where gene prediction is a bit tricky. This genome cannot be predicted by prodigal and requires manual curation.

I would like to run CrisperCasTyper against this genome. Is it possible to use gbk or protein fasta and gff as input?

Best,

Keigo

Russel88 commented 1 year ago

Hi Keigo,

It is unfortunately not possible to use other input than a nucleotide fasta. But it's definitely something I should implement, but it will be some time before I have the time to implement.

Best, Jakob

pentamorfico commented 1 year ago

I've made a pull request to allow to use GFF/Protein FASTA input instead of Prodigal, but it still needs the nucleotide FASTA for CRISPR arrays identification. For now it is only working with NCBI GFF, but making it work with prodigal should be easy