[Bioperl-guts-l] bioperl commit

Jason Stajich jason at pub.open-bio.org
Sun May 9 09:05:52 EDT 2004


jason
Sun May  9 09:05:52 EDT 2004
Update of /home/repository/bioperl/bioperl-live/Bio/Tools/Phylo
In directory pub.open-bio.org:/tmp/cvs-serv14348

Modified Files:
      Tag: branch-1-4
	PAML.pm 
Log Message:
merge changes for parsing kappa to branch

bioperl-live/Bio/Tools/Phylo PAML.pm,1.17,1.17.2.1
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Phylo/PAML.pm,v
retrieving revision 1.17
retrieving revision 1.17.2.1
diff -u -r1.17 -r1.17.2.1
--- /home/repository/bioperl/bioperl-live/Bio/Tools/Phylo/PAML.pm	2003/11/19 23:39:33	1.17
+++ /home/repository/bioperl/bioperl-live/Bio/Tools/Phylo/PAML.pm	2004/05/09 13:05:52	1.17.2.1
@@ -649,7 +649,7 @@
 sub _parse_PairwiseCodon {
     my ($self) = @_;
     my @result;
-    my ($a,$b,$log,$model);
+    my ($a,$b,$log,$model,$t,$kappa,$omega);
     while( defined( $_ = $self->_readline) ) {
 	if( /^pairwise comparison, codon frequencies\:\s*(\S+)\./) {
 	    $model = $1;
@@ -657,6 +657,10 @@
 	    ($a,$b) = ($1,$3);
 	} elsif( /^lnL\s+\=\s*(\-?\d+(\.\d+)?)/ ) {
 	    $log = $1;
+	    if( defined( $_ = $self->_readline) ) {
+		s/^\s+//;
+		($t,$kappa,$omega) = split;
+	    }
 	} elsif( m/^t\=\s*(\d+(\.\d+)?)\s+
 		 S\=\s*(\d+(\.\d+)?)\s+
 		 N\=\s*(\d+(\.\d+)?)\s+
@@ -665,10 +669,11 @@
 		 dS\=\s*(\d+(\.\d+)?)/ox ) {
 	    $result[$b-1]->[$a-1] = { 
 		'lnL' => $log,
-		't' => $1,
+		't' => $t,
 		'S' => $3,
 		'N' => $5,
-		'omega' => $7,
+		'kappa' => $kappa,
+		'omega' => $omega,
 		'dN' => $9,
 		'dS' => $11 };
 	} elsif( /^\s+$/ ) { 



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