[Bioperl-l] clustalw alignment display format

[Shawn Hoon]

You want to use Bio::AlignIO.


use Bio::AlignIO;
use Bio::Tools::Run::Alignment::Clustalw;

  my $factory = Bio::Tools::Run::Alignment::Clustalw->new();
  $inputfilename = 't/data/cysprot.fa';
  $aln = $factory->align($inputfilename); # $aln is a SimpleAlign object.

  my $aio = Bio::AlignIO->new(-fh=>\*STDOUT,-format=>'clustalw');
  $aio->write_aln($aln);

replace clustalw with any other multiple alignment
format that can be found in Bio/AlignIO/

hth,

shawn




On Sun, 7 Sep 2003, Jack Chen wrote:

> Hi, 
> 
> I have checked the BioPerl API but could not find a module that can
> display the output of clustalw alignment. This site: 
> 
> http://embnet.cifn.unam.mx/perl-doc/Bio/SimpleAlign.html
> 
> indicates that the subroutines has been implemented before but not in the
> BioPerl package yet. Any module in BioPerl can do the display?
> 
> Thanks
> 
> Jack
> 
> ++++++++++++++++++++++++++++++++++++++++++++
>     o-o     Jack Chen, Stein Laboratory      
>     o---o   Cold Spring Harbor Laboratory    
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>  0--o       Tel: 1 516 367 8394              
>    O        e-mail: chenn at cshl.org  	    
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> +++++++++++++++++++++++++++++++++++++++++++++
>         
> 
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-- 
********************************
* Shawn Hoon
* http://www.fugu-sg.org/~shawnh
********************************