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

Tao Zhu tzhu at mail.bnu.edu.cn
Thu Oct 28 03:38:55 EDT 2010


Dear Chris,

Thank you for correcting the HOWTO, but in fact it hasn't been
completely correct yet. I've made some changes to the passage again like
this,

************************
use Bio::DB::Fasta; 
($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",11250,11333);
$db = Bio::DB::Fasta->new($file);
$seq = $db->seq($id,$start,$end);
print $seq,"\n";
************************

The original passage is like this,
************************
use Bio::DB::Fasta;
($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",11250,11333);
$db = Bio::DB::Fasta->new($file);
$seqobj = $db->seq($id,$start,$end); 
print $seqobj->seq;
************************

We should notice that if method '$db->seq()' is called, then it would
return a simple string, not a Bio::Seq object.



在 2010-10-27三的 13:40 -0500,Chris Fields写道:
> 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
> 
> 





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