[Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo PAML.pm,1.33,1.34

Albert Vilella avilella at pub.open-bio.org
Mon Jan 16 10:31:34 EST 2006


Update of /home/repository/bioperl/bioperl-live/Bio/Tools/Phylo
In directory pub.open-bio.org:/tmp/cvs-serv13403

Modified Files:
	PAML.pm 
Log Message:
added parsing for beta_w1


Index: PAML.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Phylo/PAML.pm,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** PAML.pm	11 Jan 2006 15:05:06 -0000	1.33
--- PAML.pm	16 Jan 2006 15:31:32 -0000	1.34
***************
*** 992,996 ****
  		    'q'     => $2 };
  	    } else {
! 		$self->warn("unparseable beta paramters: $_");
  	    }
  	}  elsif( /^alpha\s+\(gamma\)\s+\=\s+(\S+)/ ) {
--- 992,1020 ----
  		    'q'     => $2 };
  	    } else {
! 		$self->warn("unparseable beta parameters: $_");
! 	    }
! 	} elsif( /^Parameters in beta\&w\>1:/ ) {
!             # Parameters in beta&w>1:
!             #   p0=  1.00000  p=  0.07642 q=  0.85550
!             #  (p1=  0.00000) w=  1.00000
! 	    $_ = $self->_readline; # need the next line
!             my ($p0,$p,$q,$p1,$w);
! 	    if ( /p0\=\s+(\S+)\s+p\=\s+(\S+)\s+q\=\s+(\S+)/ ) {
!                 $p0 = $1; $p = $2; $q = $3;
! 	    } else {
! 		$self->warn("unparseable beta parameters: $_");
! 	    }
! 	    $_ = $self->_readline; # need the next line
! 	    if ( /\(p1\=\s+(\S+)\)\s+w\=\s+(\S+)/ ) {
!                 $p1 = $1; $w = $2;
! 		$data{'-shape_params'} = { 
! 		    'shape' => 'beta',
! 		    'p0'    => $p0,
! 		    'p'     => $p,
! 		    'p'     => $q,
! 		    'p1'    => $p1,
!                     'w'     => $w };
! 	    } else {
! 		$self->warn("unparseable beta parameters: $_");
  	    }
  	}  elsif( /^alpha\s+\(gamma\)\s+\=\s+(\S+)/ ) {



More information about the Bioperl-guts-l mailing list