[Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo PAML.pm,1.51,1.52

Brian Osborne bosborne at dev.open-bio.org
Sun Oct 29 09:19:19 EST 2006


Update of /home/repository/bioperl/bioperl-live/Bio/Tools/Phylo
In directory dev.open-bio.org:/tmp/cvs-serv18553/Bio/Tools/Phylo

Modified Files:
	PAML.pm 
Log Message:
Move get_posteriors comments to TO DO section

Index: PAML.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Phylo/PAML.pm,v
retrieving revision 1.51
retrieving revision 1.52
diff -C2 -d -r1.51 -r1.52
*** PAML.pm	4 Oct 2006 05:52:06 -0000	1.51
--- PAML.pm	29 Oct 2006 14:19:17 -0000	1.52
***************
*** 81,85 ****
       # inspect the tree: the "t" (time) parameter is available via
       # $node->branch_length(); all other branch-specific parameters
!      # ("omega", "dN", etc.) are available via ($omega) = $node->get_tag_values('omega');
    }
  
--- 81,86 ----
       # inspect the tree: the "t" (time) parameter is available via
       # $node->branch_length(); all other branch-specific parameters
!      # ("omega", "dN", etc.) are available via 
!      # ($omega) = $node->get_tag_values('omega');
    }
  
***************
*** 90,98 ****
    printf "M1 params: p0 = %g\tp1 = %g\n", $params->{p0}, $params->{p1};
  
-   # for NSsites models, obtain arrayrefs of posterior probabilities
-   # for membership in each class for every position; probabilities
-   # correspond to classes w0, w1, ... etc.
-   my @probs = $result->get_posteriors();
- 
    # find, say, positively selected sites!
    if ($params->{w2} > 1) {
--- 91,94 ----
***************
*** 106,115 ****
    } else { print "No positive selection found!\n"; }
  
- 
    # parse AAML result files
    my $aamat = $result->get_AADistMatrix();
    my $aaMLmat = $result->get_AAMLDistMatrix();
  
- 
  =head1 DESCRIPTION
  
--- 102,109 ----
***************
*** 119,122 ****
--- 113,124 ----
  PAML programs, but this module is only useful to parse the output.
  
+ =head1 TO DO
+ 
+ Implement get_posteriors(). For NSsites models, obtain arrayrefs of 
+ posterior probabilities for membership in each class for every 
+ position; probabilities correspond to classes w0, w1, ... etc.
+ 
+   my @probs = $result->get_posteriors();
+ 
  =head1 FEEDBACK
  



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