BioPerl Mailing List Summaries April 11, 2006
The first of a biweekly summary of BioPerl mailing list summaries has been posted to the wiki:
These will likely be archived on the wiki but may be moved to a more suitable location in the future (maybe to this blog?).
- Posted in : Documentation, Code, Development, Community, Mailing lists
- Author : Chris Fields
Comments»
I just coded according to howto manual
but I can’t get any result. there is no error message~!~
what’s happen??
use lib “/usr/local/lib/perl5/site_perl/5.8.7″;
use Bio::Tools::Run::Phylo::PAML::Yn00;
use Bio::AlignIO;
my $alignio = new Bio::AlignIO(-format => ‘phylip’,
-file => ‘/r1/people/daewon_kim/ Oranutan_cDNA/2.Processing/4.CodonC/dNdSGene1.phylip’,
-idlength=>12,
-interleaved => 1);
my $aln = $alignio->next_aln;
my $yn = new Bio::Tools::Run::Phylo::PAML::Yn00();
$yn->alignment($aln);
my ($rc,$parser) = $yn->run();
if(my $result = $parser->next_result) {
my @otus = $result->get_seqs();
my $MLmatrix = $result->get_MLmatrix();
# 0 and 1 correspond to the 1st and 2nd entry in the @otus array
my $dN = $MLmatrix->[0]->[1]->{dN};
my $dS = $MLmatrix->[0]->[1]->{dS};
my $kaks =$MLmatrix->[0]->[1]->{omega};
print “Ka = $dN Ks = $dS Ka/Ks = $kaks\n”;
}
You should be posting this to the mail list and not here:
http://bioperl.org/mailman/listinfo/bioperl-l
BTW, Bio::Tools::Run::Phylo::PAML::Yn00/codeml were recently updated to deal with results from PAML 3.15 which could be your problem, but you’ll have to update from CVS.