[Bioperl-l] question on simple align object
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.
More information about the Bioperl-l