[Bioperl-l] Locatable sequence with numbers

[Heikki Lehvaslaiho]

Ian,

You could use Bio::Seq::Meta to store the mask, but  
Bio::Tools::Run::Alignment::Clustalw would not know about your mask encoded 
into the sequence object, so you'd have to modify its code to actually pass 
the mask to clustalw.

	-Heikki


On Monday 08 Mar 2004 16:57, Iain Wallace wrote:
> Hi
>
> I am trying to create a file for clustalw that is of that includes the
> secondary structure mask
>
> !GM_id 1111144444411
> id     GVPINVSCTGSPQ
>
> My problem is that the code below doesn't work as $gap_mask is a string
> of numbers, and not a proper sequence.
>
>  my $newseq1 = new Bio::LocatableSeq(-seq => $gap_mask,
>                                         -id => "!GM_".$seq->id,
>                                         -start => 1,
>                                         -end => $seq->length());
>         print "adding id:\t",$seq->id,"\n";
>         $Align->add_seq($newseq1);
>
> The error that gets generated is
>
> -------------------- WARNING ---------------------
> MSG: seq doesn't validate, mismatch is 1
> ---------------------------------------------------
>
> ------------- EXCEPTION  -------------
> MSG: Attempting to set the sequence to
> [12211111114444444444412222222112222221] which does not look healthy
> STACK Bio::PrimarySeq::seq
> /usr/lib/perl5/site_perl/5.8.0/Bio/PrimarySeq.pm:268
> STACK Bio::PrimarySeq::new
> /usr/lib/perl5/site_perl/5.8.0/Bio/PrimarySeq.pm:217
> STACK Bio::LocatableSeq::new
> /usr/lib/perl5/site_perl/5.8.0/Bio/LocatableSeq.pm:100
> STACK toplevel ./dssp.pl:61
>
> --------------------------------------
>
>
> Does anyone know how I could get around this ?
>
> Thanks
>
> Iain
>
>
>
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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