[Bioperl-l] problem unigene parsing

[Andrew Macgregor]

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?


   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
>
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>
>
___________________________________________
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
___________________________________________