Bio::Restriction::Analysis::fragment does not check if enzyme exists

[fgvieira]

Dear all,

I tried using the fragments function, but it was not cutting. After some looking around. I found out Bioperl does not check if the enzyme exists!

For example:

use Bio::SeqIO;
use Bio::Restriction::Analysis;

$seqio=Bio::SeqIO->new(-file=>'dna1.fa', -format=>'fasta');
$seq=$seqio->next_seq;
$ra = Bio::Restriction::Analysis->new(-seq=>$seq);

foreach $frag ($ra->fragments('RsaI')){
    print $frag."\n";
}

works fine, but if I replace RsaI for a random string, it just prints out the full sequence. Shouldn't it give an error that the enzyme was not found?

thanks,

[cjfields]

@fgvieira yes, that should check for the enzyme and fail otherwise. This should be a straightforward fix, did you want to take it on to expedite it?

[fgvieira]

sure, I can give it a try, but do you have an idea of where would be the best place to check if the enzyme exists? I could put it under fragments, but this calls fragment_maps, which in turn calls cut that in turn calls _cuts`, and so on...

I was thinking that it would be nice to include the check as "low" as possible in order to be triggered by as many routines as possible, but not sure where it would be best.

@cjfields do you have any suggestion?
thanks,