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Gmane
From: <galiantus <at> gmail.com>
Subject: Could not go on with Bio::Tools::Run::Alignment::Pal2Nal
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Tuesday 4th June 2013 05:12:45 UTC (over 3 years ago)
Dear colleagues!

I have a problem with running pal2nal wrapper. Here is entaire script, wich

I try to use:

#!/usr/bin/perl
BEGIN { $ENV{PAL2NALDIR} = 'C:\KaKs\pal2nal.v14.tar\pal2nal.v14' }
use Bio::Tools::Run::Alignment::Pal2Nal;
use Bio::SeqIO;
use Bio::AlignIO;

my $alignio = Bio::AlignIO->new(-file => 'pep.aln',
                 -format => 'Clustalw');    
my $alnpr = $alignio->next_aln;

#Input DNA sequences
$seqio = Bio::SeqIO->new(-file => 'nuc.fasta',  '-format' => 'fasta');
    
    my $DNA1 = $seqio->next_seq();
    my $DNA2 = $seqio->next_seq();

# Make a Pal2Nal factory
$factory = Bio::Tools::Run::Alignment::Pal2Nal->new();

my $alnDP = $factory->run($alnpr, [$DNA1,$DNA2]);

$out = Bio::AlignIO->new(-file => ">4paml.phy",
                         -format => "phylip" );
$out->write_aln($aln);

The warning message I recieved is:

--------------------- WARNING ---------------------
MSG: Must provide a Bio::Align::AlignI object when calling write_aln
---------------------------------------------------

What is going wrong?

I also attached both data files.

Thanks for your kindly help!

Vladimir Popov
 
CD: 14ms