[Bioperl-l] about bioperl issue

[Scott Markel]

Reginald,

I didn't see anything highlighted in red but the three strings in the
pairwise alignment display can be obtained from an HSP using

    $hsp->query_string()
    $hsp->hit_string()
    $hsp->homology_string()

Scott

Scott Markel, Ph.D.
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-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hsueh
Sent: Thursday, 10 December 2009 6:22 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] about bioperl issue
Importance: High

Dear 

The following is code. 


--------------------------------------------------------------------------------

my at params_rb = ( 'program'  => 'blastn',
            'database' => 'DB\\RB_GUS\\RB_GUS'); my $factory_rb = Bio::Tools::Run::StandAloneBlast->new(@params_rb);

my $input_rb = Bio::Seq->new(-id  =>"test_query",
                       -seq => $testline2); my $blast_report_rb = $factory_rb->blastall($input_rb);

 while (my $result_rb =  $blast_report_rb-> next_result ) {
  while (my $hit_rb = $result_rb->next_hit()){
   while (my $hsp_rb = $hit_rb->next_hsp()){
    print $hit_rb->name,"\nevalue = " ,  $hsp_rb->evalue , "\t score = " , $hsp_rb->score , "\n" ;
    #print " ",$hit->name,"\n";
   }
  }
 }

--------------------------------------------------------------------------------


I know how to get "name", "evalue" and  "score", but I don't know how  to get the word which is in red color. (or please see attachment.)
------------------------------------------------------------------------------------------------------------------
Query: 147 ctctttactcttaggtttacccgccggggtatcgtggcaaacaaggatagtttaaacaga 206
                   |||||| ||||||||||||||||||    |||| || ||||||  |||||||||||| ||
Sbjct: 114   ctcttttctcttaggtttacccgccaatatatcctgtcaaacactgatagtttaaactga 173
------------------------------------------------------------------------------------------------------------------ 
  
I will appreciate if you could tell me how to do it.
Thank you.

Reginald Hsueh