[Bioperl-l] Understanding LocatableSeq

[Ewan Birney]

On Tue, 4 Nov 2003, Wes Barris wrote:

> Hi,
>
> I am trying to create an msf alignment of several LocatableSeq objects.
> I have tried setting the "start" and "end" attributes of each LocatableSeq
> object before adding it to the alignment but the resulting sequences are
> still not aligned in the SimpleAlign object.  What am I doing wrong?
>

SimpleAlign does not automagically do the alignment - you need to call out
to Bio::Tools::Clustalw or TCoffee or something else. SimpleAlign
*represents* alignments, doesn't make them.


(it would be cute if simple align did this magically but probably would
lead to some fascinating bug-hunts as simple align booted up a full
progressive alignment engine when a sequence was added. Hmmm. Wistful
thinking...)




> #!/usr/local/bin/perl -w
> #
> #
> use strict;
> use Bio::AlignIO;
> #
> my $aln = new Bio::SimpleAlign();
> my $lseq;
> $lseq = new Bio::LocatableSeq();
> $lseq->seq('GATCGATC');
> $lseq->id('this');
> $lseq->start(1);
> $lseq->end(8);
> $aln->add_seq($lseq);
>
> $lseq = new Bio::LocatableSeq();
> $lseq->seq('ATCGAT');
> $lseq->id('that');
> $lseq->start(2);
> $lseq->end(7);
> $aln->add_seq($lseq);
>
> my $outstream = new Bio::AlignIO(-format=>'msf', -file=>">junk.msf");
> $outstream->write_aln($aln);
> undef $outstream;
>
>
> The output looks like this:
>
>
> NoName   MSF: 2  Type: N  Tue Nov  4 09:01:58 2003  Check: 00 ..
>
>   Name: this/1-8  Len:    8  Check:  2590  Weight:  1.00
>   Name: that/2-7  Len:    6  Check:  1547  Weight:  1.00
>
> //
>
> this/1-8              GATCGATC
> that/2-7              ATCGAT	<--- Should't this be shifted one position to the right?
>
>
> I am using bioperl-1.2.3.
> --
> Wes Barris
> E-Mail: Wes.Barris at csiro.au
>
>
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