branch-1-6/examples/tools/parse_codeml.pl

   1 #!/usr/bin/perl -w
   2
   3 use strict;
   4 use Bio::Tools::Phylo::PAML;
   5 use Bio::Root::IO;
   6
   7 my $parser = new Bio::Tools::Phylo::PAML(-file    => shift,
   8                                          -verbose => shift);
   9
  10 my $result = $parser->next_result;
  11 my @otus = $result->get_seqs();
  12 my $MLmatrix = $result->get_MLmatrix();
  13 my $NGmatrix = $result->get_NGmatrix();
  14
  15 # These matrices are length(@otu) x length(@otu) "strict lower
  16 # triangle" 2D-matrices, which means that the diagonal and
  17 # everything above it is undefined.  Each of the defined cells is a
  18 # hashref of estimates for "dN", "dS", "omega" (dN/dS ratio), "t",
  19 # "S" and "N".  If a ML matrix, "lnL" will also be defined.
  20
  21 @otus = $result->get_seqs();
  22 $MLmatrix = $result->get_MLmatrix();
  23 $NGmatrix = $result->get_NGmatrix();
  24 for( my $i=0;$i<scalar @$MLmatrix;$i++) {
  25         for( my $j = $i+1; $j < scalar @{$MLmatrix->[$i]}; $j++ ) {
  26                 printf "The ML omega ratio for sequences %s vs %s was: %g\n",
  27                   $otus[$i]->id, $otus[$j]->id, $MLmatrix->[$i]->[$j]->{omega};
  28         }
  29 }
  30
  31 for( my $i=0;$i<scalar @$MLmatrix;$i++) {
  32         for( my $j = $i+1; $j < scalar @{$MLmatrix->[$i]}; $j++ ) {
  33
  34                 printf "The NG omega ratio for sequences %s vs %s was: %g\n",
  35                   $otus[$i]->id, $otus[$j]->id, $NGmatrix->[$i]->[$j]->{'omega'};
  36         }
  37 }