[Bioperl-l] problem unigene parsing

Siddhartha Basu basu at pharm.sunysb.edu
Wed Mar 5 18:09:17 EST 2003


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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