[Bioperl-l] Porblems with Bio::Tools::Run::Phylo::PAML::Baseml

Daniel Jeffares dcj at sanger.ac.uk
Thu Nov 22 09:47:09 EST 2007


Hi all,

Bio::Tools::Run::Phylo::PAML::Baseml from bioperl-run 1.5.2 seems to  
be a little 'broken', at least in my hands.
First,  $bml->set_parameter('runmode', 0); does not work (sets  
runmode to -2). setting runmode to 1 is OK.
Also,  $bml->no_param_checks(1); doesn't seem to work.

The result is that the baseml.ctl file created under /tmp is not  
runnable by baseml with runmode 0. The phylip file created is run OK  
by baeml(with another .ctl file). My script & baseml.ctl below.

Hope it can be fixed,

cheers,

Dan





#!/usr/bin/perl

use Bio::Tools::Run::Phylo::PAML::Baseml;
   use Bio::AlignIO;
   my $alignio = Bio::AlignIO->new(-format => 'phylip',-file =>  
'test.phy');
   my $aln = $alignio->next_aln;

   my $bml = Bio::Tools::Run::Phylo::PAML::Baseml->new();
   $bml->alignment($aln);
   $bml->save_tempfiles(1);
   my $tempdir = $bml->tempdir();


   #set the runmode to zero
   $bml->set_parameter('runmode', 0);

   my ($rc,$parser) = $bml->run();
   system "more $tempdir/baseml.ctl";

   while( 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
   }
exit;



The baseml.ctl file produced:
seqfile = /tmp/mtV8uuwTGW/FPS5kwtXSA
outfile = mlb
fix_rho = 1
verbose = 0
noisy = 0
RateAncestor = 1
kappa = 2.5
model = 0
ndata = 5
Small_Diff = 1e-6
runmode = -2
alpha = 0
fix_kappa = 0
rho = 0
nhomo = 0
getSE = 0
cleandata = 1
fix_alpha = 1
clock = 0
Malpha = 0
ncatG = 5
fix_blength = -1
nparK = 0










Regards,

Daniel Jeffares

______________________________
Population and Comparative Genomics
Wellcome Trust Sanger Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, CB10 1SA, UK
Phone: +44(0)1223 834244 x 7297
Fax: +44 (0)1223 494919
www.sanger.ac.uk







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