[Bioperl-l] Getting Alignment Score from Bio::Tools::Run::Alignment::TCoffee

[Jason Stajich]

We don't try and parse it.  You're welcome to add code in 
Bio::AlignIO::clustalw which would do  this.  It would be very simple 
to just parse this out of the header and there is already a score 
method in Bio::SimpleAlign to store this so that in the end score would 
be available through $aln->score.

-jason

--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/


> On Apr 20, 2005, at 5:26 AM, Edward Wijaya wrote:
>
>> Hi,
>> For the above TCoffee alignment module
>>
>> Is there a way to:
>> 1. get the alignment score (any method for this)
>> 2. Pass input sequence as an array (not fasta file)
>>    e.g. input is "@seq = qw(ATCCGGA AGGGGAA)" etc.
>>
>> Below is my current working program.
>>
>> Thanks and hope to hear from you again.
>> Regards,
>> Edward WIJAYA
>>
>> __BEGIN__
>> #!/usr/bin/perl -w
>> use strict;
>> use Bio::AlignIO;
>> use Data::Dumper;
>>
>> BEGIN {$ENV{TCOFFEEDIR} = 
>> '/home/edward/MyBioTool/T-COFFEE_distribution_Version_2.03/bin/'; }
>> use Bio::Tools::Run::Alignment::TCoffee;
>>
>> my $inputfilename = "hm02r.fasta";
>> my $outfile = "tcoffee.out";
>> my @params = (
>>               '-in'    => $inputfilename,
>>               '-outfile' => $outfile,
>>           );
>> my $factory = Bio::Tools::Run::Alignment::TCoffee->new(@params);
>> my $aln = $factory->align($inputfilename);
>>
>> __END__
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>