[Bioperl-l] Problem with revcom

Mark A. Jensen maj at fortinbras.us
Fri Jul 18 02:04:14 UTC 2014


Antony,
hit_string() returns a string, not a sequence obj.

Something like

  $rc  = Bio::Seq->new( -seq => $hsp->hit_string )->revcom;

should work.
MAJ

On 2014-07-17 20:14, Antony03 wrote:
> Hello,
>
> I try to reverse complement a sequence found with fasta36:
>
> 	if ( $hsp->strand('query') == -1 ) {
> my $rev_output=$hsp->hit_string->revcom();
> print "$rev_output";
>           }
>
> And I get an error like:
>
> Can't locate object method "revcom" via package
>
> Can someone know what is wrong with my code?
>
> Thanks,
>
> Antony
>
>
>
> --
> View this message in context:
> http://bioperl.996286.n3.nabble.com/Problem-with-revcom-tp17581.html
> Sent from the Bioperl-L mailing list archive at Nabble.com.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l



More information about the Bioperl-l mailing list