[Bioperl-l] Error calling alignment method
Jason Stajich
jason.stajich at gmail.com
Tue May 31 16:31:26 UTC 2011
Please provide exactly the script you are using or an exact simplified script that causes the error - we can't reproduce your problem without.
On May 31, 2011, at 4:26 AM, Lorenzo Carretero Paulet wrote:
> Hi,
>
> The last versions of my script had the typo corrected:
>
> my $kaks_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
>
> },
>
>
> );
>
>
> $kaks_factory->alignment($dna_aln);
>
>
> but still returns the same error.
> Best,
> Lorenzo
>
>
>
>
> El 27/05/11 21:45, Jason Stajich escribió:
>
>> 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
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioper... at lists.open-bio.orghttp://lists.open-bio.org/mailman/listinfo/bioperl-l
>> _______________________________________________
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>
>
> --
> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
> 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: locarpau at upvnet.upv.es
> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>
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