Allow more flexible formatting for FASTA files

[edgardomortiz]

I got multiple segmentation faults without error explanation when using caster-site or caster-pair until I removed the sequence descriptions inside my FASTA files and changed the extensions from .fna to .fas

I wonder if the formatting has to be this strict (given that FASTA allows sequence descriptions), maybe just ignore anything after the first space in the sequence names and allow any extension (.faa, .fna, etc).

Thanks! the tool works well but it took me a while figuring out why it was producing segmentation faults

Edgardo

[chaoszhang]

Hi Edgardo,

Can you do me a favor by sending me some of your FASTA files (just the header line). I will make sure it works when I release the next patch.

I think extension does not matter since my test cases usually do not have any extensions.

Best, Chao

[edgardomortiz]

Hi Chao,

Thanks for the quick response, here I include my original FASTA files, the same 10 loci in aminoacid and nucleotide. Another question, is it valid to write the full path to the files in the list file provided to caster?

Thanks,

Edgardo

nucleotide.zip aminoacid.zip

[chaoszhang]

It should be. Not sure about ~ but I used full path starting from / before and it worked. Let me know if your case does not work. I will try to fix it as well.

[chaoszhang]

I just fixed this issue in the development branch. It will be available in master branch after compiler and run time checks (within 1 hours). Feel free to try it, and close this issue or report more bugs. :)

[edgardomortiz]

excellent! thank you very much