[Bioperl-l] about bioperl issue
Scott Markel
SMarkel at accelrys.com
Thu Dec 10 14:47:36 UTC 2009
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
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