[From nobody Tue Sep 19 18:16:55 2006
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Subject: Help with consense module
Date: Mon, 18 Sep 2006 15:29:59 -0300
Message-ID: <29AC1A3F62AAF54BA71E367C6D62CEB096C4F8@alpha.ioc.fiocruz.br>
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Thread-Topic: confirm 9e68c570c38fde39e9fed0e1e7974923b77a093a
Thread-Index: AcbIafwn9SDHERDYTNeuIww58QclvwS5AgIo
From: "Kary Ann Del Carmen Soriano Ocana" <Kary@ioc.fiocruz.br>
To: <bioperl-l-request@lists.open-bio.org>

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Hello,

I need help with a consense module. I am using bioperl to run clustalw, seq=
boot, protdist(that are goingo to change by puzzle), weighbor and consense,=
 but for some reason I get this message:=20

MESSAGE 1
Can't call method "get_root_node" on an undefined value at /usr/local/biope=
rl-1.5.0/Bio/TreeIO/newick.pm line 236.

MESSAGE 2
------------- EXCEPTION  -------------
MSG: Expected a Bio::TreeI object
STACK Bio::Tools::Run::Phylo::Phylip::Consense::_setinput /usr/local/bioper=
l-run-1.4/Bio/Tools/Run/Phylo/Phylip/Consense.pm:448
STACK Bio::Tools::Run::Phylo::Phylip::Consense::run /usr/local/bioperl-run-=
1.4/Bio/Tools/Run/Phylo/Phylip/Consense.pm:331
STACK main::makePhylogenyPipeline filogenia_pipeline.pl:120
STACK main::main filogenia_pipeline.pl:61
STACK toplevel filogenia_pipeline.pl:42

--------------------------------------

I have no idea where to get started to try to solve this. Here is my object=
 with the principal reference.
Thank you for the help.

Regards
Kary

###########################################################################=
#####

#!/usr/bin/perl -w=20=20
use lib "/usr/local/bioperl-1.5.0";
use lib "/usr/local/bioperl-run-1.4";
use Bio::Tools::Run::Alignment::Clustalw;
use Bio::Tools::Run::Phylo::Phylip::SeqBoot;
use Bio::Tools::Run::Phylo::Phylip::ProtDist;
use Bio::Tools::Run::Phylo::Phylip::Neighbor;
use Bio::Tools::Run::AnalysisFactory::Pise;
use Bio::Tools::Run::Phylo::Phylip::Consense;
use Bio::Tools::Run::Phylo::Phylip::DrawTree;
use Bio::AlignIO;
use Bio::SimpleAlign;
use strict;

################## dir #########################

sub makePhylogenyPipeline{
  my $dirin_mafft	=3D $_[0];=20
  my $length_weighbor	=3D $_[1];=09=09=09=09
  my $inputfilename	=3D "";

  &makeInvariantAwk($length_weighbor);=20

  open (READDIRMOD, "find $dirin_mafft |") or die "Cannot open $dirin_mafft=
: $!";
=20=20
  while ($inputfilename =3D <READDIRMOD>){=20
    for ($inputfilename =3D~ /\.mafft$/) {
      $inputfilename =3D~ s/\n//;=20=20=20=20=20
#Create a SimpleAlign object
      my @params_align =3D (	'ktuple' =3D> 2,=20
  				'matrix' =3D> 'BLOSUM',
				'output' =3D> 'PHYLIP',
				'outfile' =3D> $inputfilename.'.phy');

       my $factory =3D Bio::Tools::Run::Alignment::Clustalw->new(@params_al=
ign);
       my $aln =3D $factory->align($inputfilename); 			# $aln is a SimpleAl=
ign object.

#Use seqboot to generate bootstrap alignments
  my @params =3D (	'datatype'=3D>'SEQUENCE',
#			'replicates'=3D>1000);
			'replicates'=3D>1);
  my $seqboot_factory =3D Bio::Tools::Run::Phylo::Phylip::SeqBoot->new(@par=
ams);
  my $aln_ref =3D $seqboot_factory->run($aln);

#next build distance matrices=20
  my @params_protdist =3D ('MODEL' =3D> 'PAM');
  my $protdist_factory =3D Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@p=
arams_protdist);

#next construct trees
  #Build a Pise factory
  my $weighbor_factory =3D new Bio::Tools::Run::AnalysisFactory::Pise();=20=
=20

  #Then create an application object (Pise::Run::Tools::PiseApplication):
  my $weighbor =3D $weighbor_factory->program('weighbor');

  my @tree;

  foreach my $a (@{$aln_ref}){
    my $matrix =3D $protdist_factory->create_distance_matrix($a);
    push @tree, $weighbor->run('infile' =3D> $matrix,
			       'length' =3D> 500,=09=09=09
 			       'size'   =3D> 3.85);		# Size of the alphabet (-b)
=20=20
  }=20=20=20=20=20=20=20

#use consense to get a final tree
  my $consense_factory =3D Bio::Tools::Run::Phylo::Phylip::Consense->new();
  my ($tree) =3D $consense_factory->run(\@tree);
=20=20
#now draw the tree
  my $draw_factory =3D Bio::Tools::Run::Phylo::Phylip::DrawTree->new();
  my $image_filename =3D $draw_factory->draw_tree($tree);

    }=20=20=20=20
  }
  close (READDIRMOD);



}







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