[Bioperl-l] problem unigene parsing

[Hilmar Lapp]

I guess it's a left-over from a debugging session. I removed it. This 
is not present on the 1.2 branch.

	-hilmar

On Wednesday, March 5, 2003, at 05:50  PM, 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?
>
>
>   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
> ___________________________________________
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------