[MOBY-dev] Strange problems with nested moby objects

[Edward Kawas]

Hi,

The problem is with your line

my $newTranscript => new MOSES::MOBY::Data::SNPTranscript

that should actually read

my $newTranscript = new MOSES::MOBY::Data::SNPTranscript

an equal sign not a =>

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Volker Rössler
Sent: Monday, November 15, 2010 3:32 AM
To: moby-dev at lists.open-bio.org
Subject: [MOBY-dev] Strange problems with nested moby objects

Hi everyone,

I'm experiencing a rather strange problem when trying to build the response
object. What I'd like to achieve is building an
'AnnotatedSNPAndTranscriptLocation' object which contains an array of
'SNPTranscript' objects.

My code for building the response object looks like this, but this causes
some strange problems:


@SNP_list = mymethod($some_user_input);

foreach my $SNP (@SNP_list) {

        my @listOfBiomobyTranscriptObjects;

        my $transcriptList = $SNP->get_transcript_list();

        foreach my $trans (@$transcriptList) {

            my $snp_type = $trans->get_field('snp_type');
            my $database_references = new MOSES::MOBY::Data::Object
                (
                    id => $trans->get_field('name'),
                    namespace => 'Ensembl'
                );
            my $strand = $trans->get_field('strand');
            my $description = $trans->get_field('description');
            my $name = $trans->get_field('name');
            my $start = $trans->get_field('start');
            my $stop = $trans->get_field('stop');


            my $newTranscript => new MOSES::MOBY::Data::SNPTranscript
                (
                    snp_type => $snp_type,
                    #database_references => $database_references,
                    strand => $strand,
                    description => $description,
                    name => $name,
                    start => $start,
                    stop => $stop
                );
            push (@listOfBiomobyTranscriptObjects, $newTranscript);
        }

        my $output_snp_transcripts = new
MOSES::MOBY::Data::AnnotatedSNPAndTranscriptLocation
            (

                snp_transcripts => \@listOfBiomobyTranscriptObjects,
                coverage_all => $SNP->get_snp_coverage_all(),
                coverage_new_allele => $SNP->get_snp_coverage_new_allele(),
                genetype_allele => $SNP->get_snp_genotype_allele(),
                reference_allele => $SNP->get_snp_reference_allele(),
                confidence => $SNP->get_snp_score(),
                Position => new MOSES::MOBY::Data::Position
                    (
                        end => $SNP->get_snp_position(),
                        start => $SNP->get_snp_position(),
                        chromosome => $SNP->get_snp_chromosome()
                    ),
                Strain => $strain
            );
        $response->add_output_snp_transcripts($output_snp_transcripts);
    }



When I'm trying to run this, I get the following error message:
2010/11/15 12:26:02 (71764) FATAL> [13065] (eval 1068):155 -
------------- EXCEPTION: MOSES::MOBY::Data::SNPTranscript -------------
MSG: No such method: MOSES::MOBY::Data::SNPTranscript::value

I suspect, that this error happens, because I am trying to use an array of
MOSES::MOBY::Data::Object (stored in @listOfBiomobyTranscriptObjects), but
I'm not quite sure.

Any help or suggestions are greaty appreciated!

Yours,
Volker
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