[Bioperl-l] undef query_len error with Bio::Search::Hit::GenericHit::num_unaligned_query

Jason Stajich jason at bioperl.org
Thu Jun 8 16:15:47 EDT 2006


why are you trying to create new Hit objects?
  $hit_obj is-A GenericHit object...


-jason
On Jun 8, 2006, at 1:12 PM, Freimuth, Robert wrote:

> Hi,
>
> I'm trying to use the Bio::Search::Hit::GenericHit class to tile a set
> of hits from blast, then get some information about the tiled  
> result.  I
> thought I'd use the num_unaligned_query and num_unaligned_hit  
> methods to
> get the number of unaligned bases in the tiled result, then subtract
> that from the length of the query/subject sequence to get the  
> number of
> aligned bases in the region spanned by the hit(s).  My code is below,
> followed by the error message.
>
>
> while( my $result_obj = $blast_obj->next_result() )
> {
>     while( my $hit_obj = $result_obj->next_hit() )
>     {
>         my $generic_hit_obj = Bio::Search::Hit::GenericHit->new( -name
> => $hit_obj->name() );
>         $generic_hit_obj->overlap( 0 ); # tile any hsps that overlap >
> this number of bp
>
>         while( my $hsp_obj = $hit_obj->next_hsp() )
>         {
>             # add all HSPs to a GenericHit object so they can be tiled
> together
>             $generic_hit_obj->add_hsp( $hsp_obj );
>         }
>
>         my $num_unaligned_query =
> $generic_hit_obj->num_unaligned_query();
>         my $num_unaligned_hit = $generic_hit_obj->num_unaligned_hit();
>
>
>
> ------------- EXCEPTION  -------------
> MSG: Must have defined query_len
> STACK Bio::Search::Hit::GenericHit::logical_length
> /usr/lib/perl5/site_perl/5.8.0/Bio/Search/Hit/GenericHit.pm:698
> STACK Bio::Search::Hit::GenericHit::num_unaligned_query
> /usr/lib/perl5/site_perl/5.8.0/Bio/Search/Hit/GenericHit.pm:1264
> STACK main::process_blast_hit blast_needle_timetrials_1.pl:245
> STACK toplevel blast_needle_timetrials_1.pl:94
>
> --------------------------------------
>
>
> I looked through the docs to try to find an explanation or some  
> mention
> of how to set query_len, but I didn't find anything.  Could someone
> please point out what I'm doing wrong?  Additionally, if I'm making  
> this
> harder than it needs to be, please give me a gentle whack with the  
> clue
> stick.
>
> Thanks,
> Bob
>
>
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12




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