[Bioperl-l] Understanding LocatableSeq

[Wes Barris]

Ewan Birney wrote:

> 
> 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.

I know that SimpleAlign does not automagically do the alignment.  That
is why I am setting the "start" and "end" attributes.  I have an ACE
file from clustal.  I am trying to write an msf file.  I have the
sequences and the alignment information.  Now I want to write this
into a SimpleAlign object.

> 
> 
> (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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>>


-- 
Wes Barris
E-Mail: Wes.Barris at csiro.au