Add option to provide fasta of sequences to hunt command

[bricoletc]

Hello! Thanks for this great tool.

I'm using dicey hunt to check for uniqueness of primers in my target genome, and would like to do it in routine on a set of sequences, instead of one by one - could you/we add this as an input CLI parameter?

Best,
Brice

[tobiasrausch]

Hi Brice,

For primer searches we developed dicey search and the web application silica because this subcommand includes Tm calculations, primer hits and amplicon predictions and this tool accepts a multi-FASTA file. Why is that subcommand not applicable for you?

Best, Tobias

[bricoletc]

IIUC, running dicey search will both match primers to the genome, and attempt to find amplicons from primer pairs - right? I wasn't specific enough: here I'm actually working on a set of sequences (that I called 'primers') that I don't want to get amplicons for - I just want to know where they match in the genome. So I suppose running search is a bit wasteful in that sense; but I could just focus on the primers part of the JSON output of search?

[bricoletc]

Though because search can take a FASTA, I assume hunt could pretty easily too in theory!

[tobiasrausch]

Sure, I write that down as an enhancement for the future. Thanks for the suggestion!