[Bioperl-l] problem unigene parsing

[Ewan Birney]

On Thu, 6 Mar 2003, Andrew Macgregor wrote:

> Hi Siddhartha,
>
> Yes I can reproduce this problem. When a Unigene object is created it
> uses Species.pm that has this code segment that seems to print the
> message you are getting (I think). Can anyone else help me out as to
> why this is happening?

Looks like a debugging message which can be commented out. This is what
happens when you use bleeding edge code ;)


>
>
>    if( defined $classification &&
>        (ref($classification) eq "ARRAY") ) {
>        print "classification was @$classification\n";
>        $self->classification(@$classification);
>    }
>
> -- Andrew.
>
>
>
> On Thursday, March 6, 2003, at 12:09  PM, Siddhartha Basu wrote:
>
> > Hi,
> > I am getting some erroneous output while trying to parse the latest
> > unigene build file using the bioperl unigene parser. I am using the
> > latest bioperl code from the cvs.
> >
> > Here is the my perl code
> >
> > #####################
> > #!/usr/bin/perl -w
> >
> > use strict;
> > use Bio::Cluster::UniGene;
> > use Bio::ClusterIO;
> >
> > my $Stream = Bio::ClusterIO->new( '-file' => 'Hs.dat' '-format' =>
> > 'unigene');
> >
> >         while (my $Data = $Stream->next_cluster()) {
> >
> >                 print $Data->unigene_id(),"\n";
> >                 print $Data->gene(),"\n" if $Data->gene();
> >                 while (my $LocusLink = $Data->next_locuslink()) {
> >                         print $LocusLink,"\n";
> >                         }
> > }
> >
> > ################################
> >
> > It's printing the unigene_id,gene name and locuslink no.for each
> > unigene entry but it's also printing the line
> > "classification was sapiens Homo" with each of the above value.
> > The same type of output is also coming if i use the rat, mouse or
> > drosophila unigene build file.
> > For rat file the output is "classification was norvegicus Rattus".
> > For mouse file the output is "classification was musculus Mus".
> > However, this is not occuring in case of C.elegans file.
> >
> > The output is still coming even if i comment out those print
> > statements.
> >
> > So, what exactly is happening with my code so that i am getting this
> > unwanted output.
> > .
> >
> > Thanks in advance.
> >
> > Siddhartha
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
> >
> ___________________________________________
> Andrew Macgregor
> Bioinformatics Programmer & Database Administrator
> Molecular Embryology Group
> Department of Anatomy & Structural Biology
> University of Otago, Dunedin, New Zealand
> andrew.macgregor at stonebow.otago.ac.nz
> Telephone: +64 3 479 7873
> http://anatomy.otago.ac.nz/meg
> ___________________________________________
>
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