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NBISweden / GAAS

Genome Assembly and Annotation Service code
GNU General Public License v3.0
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Bug in gaas_filter_by_size.pl #61

Closed marchoeppner closed 3 years ago

marchoeppner commented 3 years ago

Hi,

in: gaas_filter_by_size.pl

you guys are not actually using the "-o" option to designate an output file. And in addition, the line used to name the output file has an error in the regexp:

/.fa/ -> should be /\.fa/

However, I was actually annotating some dog data, with the file name "Canis_familiaris.proteins.fa" - and that actually produced:

Canisamiliaris.proteins.30.fa

Obviously, this is a problem for nextflow or other tools using name tracking. So maybe just use the "-o" option so users can choose the name.

Juke34 commented 3 years ago

Hi, Yes changing the ouput file was bad bad bad.... my fault I remove it. But to go from Canis_familiaris.proteins.fa to Canisamiliaris.proteins.30.fa I don't see. It is probably not that script... Could you check?

marchoeppner commented 3 years ago

Thanks!

I think the naming issues comes from the regexp. The way is written now is "any character followed by 'fa'. It should be "dot character followd by fa" - so the dot needs to be escaped.

Anyway, thanks for fixing it!

Juke34 commented 3 years ago

Oh Yes I didn't see the fa from familiaris removed, I was looking at the .proteins.30 that was added ^^