[Bioperl-l] ace to msf format?

[Brian Osborne]

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.

-----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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