[Bioperl-l] question on simple align object

Michael Cipriano mcipriano at mbl.edu
Fri Feb 6 16:43:59 EST 2004

Is there a way I can get a Simple Alignment object that I created from a
clustalw alignment into a string of a specific format? I do not want to
deal with any files at all, I want to just be able to print the
alignment from a cgi-script on a web page.

So far I have this:

# Create alignment
my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);

my $aln = $factory->align($seq_array_ref);

I tried all sorts of things, but can't get specifically what I need
(which is simply the whole alignment file as a msf formated string). I
would like to not have to deal with any temporary files, unless there is
a way I can get to the temporary file that is created from the clustalw
alignment and just stick that into a string.

Thanks for any help in advance.

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