[Bioperl-l] problem unigene parsing

[Andrew Macgregor]

Hi Siddhartha,

I'm not too sure what's causing that problem - I'll see if I can 
reproduce it. However, I took your script and made one change and it 
works fine on my setup.

> my $Stream = Bio::ClusterIO->new( '-file' => 'Hs.dat', '-format' => 
> 'unigene');
										-----

I just added a comma after 'Hs.dat' - also did you rename the file, as 
the unigene files are normally called Hs.data.

Cheers, 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
___________________________________________