[Bioperl-l] ace to msf format?

[Wes Barris]

Brian Osborne wrote:

> Wes,
> 
> I don't think this is possible in Bioperl. To put it more generally, AlignIO
> can't accommodate Assembly objects currently. AlignIO is the module that
> takes in a variety of alignment formats and interconverts them, analogous to
> SeqIO. I'll be corrected if I'm wrong.
> 
> Brian O.

I am kind of new to this so I could be wrong but isn't an Assembly a group
of alignments?  So, from one assemble, a group of alignments could be
generated?

> 
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Wes Barris
> Sent: Thursday, August 28, 2003 7:58 PM
> To: Bioperl Mailing List
> Subject: [Bioperl-l] ace to msf format?
> 
> Can anyone give me a hint as to how I could use bioperl to read in
> an ACE assembly and write out an MSF formatted alignment?  This shows
> what I have figured out so far:
> 
> #!/usr/local/bin/perl -w
> #
> use strict;
> use Bio::Assembly::IO;
> #
> my $usage = "Usage: $0 <infile.ace>\n";
> my $infile = shift or die $usage;
> 
> my $io = new Bio::Assembly::IO(-file=>$infile, -format=>'ace');
> my $assembly = $io->next_assembly;
> 
> my $aln = $assembly->all_contigs();
> 
> --
> Wes Barris
> E-Mail: Wes.Barris at csiro.au
> 
> 
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> 


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