[Bioperl-l] A problem on BioPerl module Bio::DB::Fasta

Chris Fields cjfields at illinois.edu
Wed Oct 27 14:40:02 EDT 2010


Tao,

I've made that correction to the HOWTO.  In the future, if you see an error on the wiki you are free to make changes to correct them.  

Thanks!

chris

On Oct 26, 2010, at 8:08 PM, Tao Zhu wrote:

> Hello, everyone!
> 
> I hope it isn't true, but I really find a problem on BioPerl module
> Bio::DB::Fasta. In http://www.bioperl.org/wiki/HOWTO:Beginners Brian
> Osborne wrote that we could catch sub-sequences like this,
> 
> 
> use Bio::DB::Fasta;
> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
> $db = Bio::DB::Fasta->new($file);
> $seqobj = $db->get_Seq_by_id($id,$start,$end);
> print $seqobj->seq,"\n";
> 
> 
> In fact it didn't work. I only got the whole sequence after running the
> script. Therefore I referred to the Pdoc documentation and realized it
> should be written as follows,
> 
> 
> use Bio::DB::Fasta;
> ($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
> $db = Bio::DB::Fasta->new($file);
> $seq = $db->seq($id,$start,$end);
> print $seq,"\n";
> 
> 
> Then it would return the sub-sequence from 6 to 10.
> 
> Probably Dr Osborne had made a mistake when writing the use-guide
> HOWTO:Beginners.
> 
> 
> -- 
> Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> 100875, China
> email: tzhu at mail.bnu.edu.cn
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




More information about the Bioperl-l mailing list