feature request - allow for user to define output prefix and/or output directory

[kapsakcj]

It would be nice for the user to be able to define at the minimum the output filename prefix with an option like --outprefix <string> and even better, define the output directory with an option like --outdir <directory>. It would allow for more flexibility and predictablity of output filenames, which is useful for incorporation of agrvate into workflows.

AFAIK agrvate currently uses the filename prefix to name the output directory and resulting file names. Looks to me like it is cutting on the period, but perhaps I'm misunderstanding the code here: https://github.com/VishnuRaghuram94/AgrVATE/blob/main/agrvate#L138

$ agrvate -i asdfasdf12345.fasta -m
Processing asdfasdf12345.fasta ...
/usr/local/bin/agrvate_databases/ is valid
agr typing successful, gp1
Mummer successful
Extracting agr operon from mummer output
Mummer alignment is contiguous
agr operon extraction successful
Snippy successful
No frameshifts found

$ tree -L 1 asdfasdf12345-results/
asdfasdf12345-results/
├── asdfasdf12345-agr_gp.tab
├── asdfasdf12345-agr_operon.fna
├── asdfasdf12345-agr_operon_frameshifts.tab
├── asdfasdf12345-blastn_log.txt
├── asdfasdf12345-mummer
├── asdfasdf12345-mummer-log.txt
├── asdfasdf12345-snippy
├── asdfasdf12345-snippy-log.txt
└── asdfasdf12345-summary.tab

[VishnuRaghuram94]

Thank you for the feature idea! I think I will be able to implement it (albeit I cannot provide a timeline as the bulk of my attention is on another project at the moment). Currently yes AgrVATE cuts at the last period. I can still keep that behavior as the default while providing the option to name the output dir and also have a prefix.

[kapsakcj]

Sounds good and no worries on the timeline, just something to put on the roadmap for the next version 👍