[Bioperl-l] LocatableSeq::subseq(): bug or not?

[Mark A. Jensen]

Bug #2682 contains a patch that modifies subseq() to strip gaps if 
desired. It also tries to fix the $replace weirdness.

perldb transcript:
  DB<11> $seq  = new Bio::PrimarySeq(-seq=>'--atg---gta--')

  DB<12> x $seq->subseq(1,3)
0  '--a'
  DB<13> x $seq->subseq(1,3,NOGAP)
0  'a'
  DB<15> x $seq->seq
0  '--atg---gta--'
  DB<16> x $seq->subseq(-START=>1, -END=>3, -REPLACE_WITH=>'tga')
0  '--a'
  DB<18> x $seq->seq
0  'tgatg---gta--'
## silly gap-stripper:
  DB<21> x $seq->subseq(-START=>1, -END=>$seq->length,
                                          -REPLACE_WITH=>$seq->subseq(-START=>1,
                                                                       
                              -END=>$seq->length,
                                                                       
                              -NOGAP=>1))
0  'tgatg---gta--'
  DB<22> x $seq->seq
0  'tgatggta'

----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "BioPerl List" <bioperl-l at lists.open-bio.org>
Sent: Sunday, November 23, 2008 7:31 PM
Subject: [Bioperl-l] LocatableSeq::subseq(): bug or not?


> Currently, we have Bio::LocatableSeq use the default 
> (Bio::PrimarySeq)  implementation of subseq().  However the returned 
> data apparently  clashes with the actual PrimarySeq documentation:
>
>  Function: returns the subseq from start to end, where the first 
> base
>            is 1 and the number is inclusive, ie 1-2 are the first 
> two
>            bases of the sequence
>
> So, should the following actually return the indicated range of 
> bases  (no gaps)?  Or should we clarify the above documentation to 
> indicate  subseq() returns the first x positions/columns (anything) 
> instead of  'bases' (no gaps)?
>
> my $seq = Bio::LocatableSeq->new(
>    -seq => '--atg---gta--',
>    -strand => 1,
>    -start => 1,
>    -end => 6,
>    -alphabet => 'dna'
> );
>
> # comments indicate current returned val
> $seq->subseq(1,3);  # returns '--a'
> $seq->subseq(3,6);  # returns 'atg-'
> $seq->subseq(1,10); # returns '--atg---gt'
>
> chris
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