[Bioperl-l] Error calling alignment method

[Jason Stajich]

Lorenzo -

The problem is not that $dna_alignment is not defined - that is not
what the error message is saying.
It is saying you can't call 'alignment' on an undefined value

This is the line:
  my $kaks_factory->alignment($dna_aln);
Should be
 $ks_factory->alignment($dna_aln);

If you star with the simple code in the perldoc you can see how the
steps are intended to be run.
         my $codeml = Bio::Tools::Run::Phylo::PAML::Codeml->new();
         $codeml->alignment($aln);
         my ($rc,$parser) = $codeml->run();
         my $result = $parser->next_result;
         my $MLmatrix = $result->get_MLmatrix();
         print "Ka = ", $MLmatrix->[0]->[1]->{'dN'},"\n";

You can also initialize the Codeml object with the alignment directly
  my $ks_factory = new Bio::Tools::Run::Phylo::PAML::Codeml(-alignment
=> $dna_aln,
               -params => .... ); # as you did before


On May 25, 10:58 am, Lorenzo Carretero Paulet <locar... at upvnet.upv.es>
wrote:
> Hi all,
> I'm trying to create the following subroutine but I get the error message:
> "Can't call method "alignment" on an undefined value at
> /Users/marioafares/Documents/workspace/PlantEvolGen/test.pl line 80,
> <GEN1> line 2."
> which indicates $dna_aln is undefined. However, I manage to print it
> using Dumper, so I guess it is actually defined.
> Can anyone see where the problem is?
> I attach the two files I'm using in the test.
> Thanks in advance,
> Lorenzo
>
>     #!/usr/local/bin/perl -w
>     use 5.010;
>     use strict;
>     use Data::Dumper;
>     # definition of the environmental variable CLUSTALDIR
>     BEGIN {$ENV{CLUSTALDIR} =
>     '/Applications/Bioinformatics/clustalw-2.1-macosx/'}
>     use Bio::Tools::Run::Alignment::Clustalw;
>     use Bio::Align::Utilities qw(aa_to_dna_aln);
>
>     BEGIN {$ENV{PAMLDIR} = '/Applications/Bioinformatics/paml44/bin/'}
>     use Bio::Tools::Run::Phylo::PAML::Codeml;
>
>     my $sequencesfilenameAA =
>     "/Users/marioafares/Documents/SequenceDatabase/plaza_public_02_Apr27/plaza_ public_02/BLAST_Parsed_results/PerSpecies/test_vs_test.par.aa.1.fas";
>
>     my $sequencesfilenameNT =
>     "/Users/marioafares/Documents/SequenceDatabase/plaza_public_02_Apr27/plaza_ public_02/BLAST_Parsed_results/PerSpecies/test_vs_test.par.nt.1.fas";
>
>     my $format = 'fasta';
>
>     GettingBioperlAlignmentAAtoDNAplusPAMLcalculation
>     ($sequencesfilenameAA, $sequencesfilenameNT, $format);
>
>     sub GettingBioperlAlignmentAAtoDNAplusPAMLcalculation
>     {
>     my ( $sequencesfilenameAA, $sequencesfilenameNT, $format, $ktuple,
>     $matrix  ) = @_;
>     my %hashNTseqs = ();
>     my $likelihood;
>     my $Ks;
>     my $Ka;
>     my $omega;
>     my $factory = Bio::Tools::Run::Alignment::Clustalw->new (); #use
>     default parameters in here
>     my $pep_aln = $factory->align($sequencesfilenameAA);
>
>     my $inseq = Bio::SeqIO->new(-file => "<$sequencesfilenameNT",
>                                  -format => $format );
>          while (my $seq = $inseq->next_seq)
>              {
>              my $seq_id = $seq->display_id();
>              $hashNTseqs{$seq_id} = $seq;
>              }
>     my $dna_aln = aa_to_dna_aln($pep_aln, \%hashNTseqs);
>     say Dumper \%hashNTseqs;
>     say Dumper $dna_aln;
>     ###########################################################
>     #my $codeml_runs = 5;
>     my $ks_factory = new Bio::Tools::Run::Phylo::PAML::Codeml
>                            (     -params =>     {
>                                                #'verbose' => 0,
>                                                #'noisy' => 0,
>                                                'runmode' => -2,
>                                               'seqtype' => 1,
>                                               #'model' => 0,
>                                               #'NSsites' => 0,
>                                               #'icode' => 0,
>                                               #'fix_alpha' => 0,
>                                               #'fix_kappa' => 0,
>                                               #'RateAncestor' => 0,
>                                              'CodonFreq' => 2,
>                                              'cleandata' => 1,
>                                              'ndata' => 1
>                                             },
>
>                            );
>
>     my $kaks_factory->alignment($dna_aln);
>
>     say "\nCalculating Ks-values of current cluster ...";
>
>          # The estimation of the Ks-values is repeated $codeml_runs
>     times ...
>     #    for(my $k=1;$k <= $codeml_runs;$k++)
>     #    {
>     #        print "\nCodeml-Run $k:\n\n";
>
>              # Ka and Ks-vlaues are calculated using codeml
>              my ($rc,$parser) = $kaks_factory->run();
>              #$kaks_factory->cleanup();
>              # If the calculation was succsessful ...
>     #        if($rc != 0)
>     #        {
>                  my $result = $parser->next_result;#not sure what it
>     does here
>                  #my $NGmatrix = $result->get_MLmatrix();
>                  my $MLmatrix = $result->get_MLmatrix();
>                      $likelihood = $MLmatrix->[0]->[1]->{'lnL'};
>                      $Ks = $MLmatrix->[0]->[1]->{'dS'};
>                      $Ka = $MLmatrix->[0]->[1]->{'dA'};
>                      $omega = $MLmatrix->[0]->[1]->{'omega'};
>                      print " likelihood = $likelihood, Ka = $Ka, Ks =
>     $Ks, Ka/Ks = $omega\n";
>     #        }
>     #        else # If an error occured during the Ks-calculation ...
>     #        {
>     #            return (-1);
>     #        }
>     #    }
>     return ( $likelihood, $Ks, $Ka, $omega );
>     }
>
> --
> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
> Lorenzo Carretero Paulet
> Institute for Plant Molecular and Cell Biology - IBMCP (CSIC-UPV)
> Integrative Systems Biology Group
> C/ Ingeniero Fausto Elio s/n.
> 46022 Valencia, Spain
>
> Phone:  +34 963879934
> Fax:    +34 963877859
> e-mail:locar... at upvnet.upv.es
> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>
>  test_vs_test.par.nt.1.fas
> 3KViewDownload
>
>  test_vs_test.par.aa.1.fas
> 1KViewDownload
>
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