[Bioperl-l] qury

Donald Jackson (Genomics) donald.jackson at bms.com
Thu Feb 21 09:01:51 EST 2008


Hi Somil,

I get the same error from my test script.  It will be a few days before 
I can troubleshoot and upload the fix to CVS; I'll let you know when 
I've posted the fix.


Don Jackson

Somil Dutt wrote:

>Hello
>
>I used the SiRNA  tool which is written below
>
>
>use Bio::Tools::SiRNA;
>
>*
>  my $sirna_designer = Bio::Tools::SiRNA->new( -target => $bio_seq,
>                                               -rules  => 'saigo'
>    );
>  my @pairs = $sirna_designer->design;
>
>  foreach $pair (@pairs) {
>      my $sense_oligo_sequence = $pair->sense->seq;
>      my $antisense_oligo_sequence = $pair->antisense->seq;
>
>      # print out results
>      print join ("\t", $pair->start, $pair->end, $pair->rank,
>                  $sense_oligo_sequence, $antisense_oligo_sequence), "\n";*
>  }
>
>
>But the following problem
>
>------------- EXCEPTION Bio::Root::BadParameter -------------
>MSG: Target must be passed as a Bio::Seq object
>STACK Bio::Tools::SiRNA::target C:/Perl/site/lib/Bio/Tools/SiRNA.pm:220
>STACK Bio::Tools::SiRNA::new C:/Perl/site/lib/Bio/Tools/SiRNA.pm:198
>STACK toplevel start.pl:32
>
>I dont understand why this error is coming.
>
>Regards
>  
>


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