[Bioperl-l] $hsp->seq_inds and axt file

[Alynne Chiromatzo]

Hi!

I'm having trouble in finding the hsp->seq_inds in the axt file(whole
genome alignment from UCSC Genome Browser). The code is below and a
sample of the input file. It doens't show the sequence that it suppose
to contain. Anyone can help me?

Thanks very much!

Alynne Oya.

#! /usr/bin/perl

use Bio::SearchIO;

 my $parser = new Bio::SearchIO(-format => 'axt',
                                 -file   => '/work/project/align/testeaxt');
 while( my $result = $parser->next_result ) {
   while( my $hit = $result->next_hit ) {
     while( my $hsp = $hit->next_hsp) {
         print "Hank: ".$hsp->rank." Strand : ".$hsp->strand('hit')."\n";
         print "Query Name: ".$result->query_name." Hit Name: ".$hit->name."\n";
         ($query_beg, $query_end) = $hsp->range('query');#encontra os
valores de inicio-final, mas soh q somados de 1
         ($hit_beg,$hit_end) = $hsp->range('hit');
         print "Range: ".($query_beg-1)."-".($query_end-1)."
".($hit_beg-1)."-".($hit_end-1)."\n";
         print $hsp->query_string."\n".$hsp->hit_string."\n";
         @h_ind = $hsp->seq_inds('query', 'identical', 1);

         #Here doesn't apper the index sequence like it suppose to show
         foreach (@h_ind){    
            print "==> ".$_." ";
         }
         print "\n";
     }

This is a sample of the input file:

1 SCAFFOLD1 1535 1688 chrX 44389546 44389697 + 6498
TACAATAGGTCAAGGGTCTGCAAACTATAGGTTTAAAAATTAAAAAGAA-GAAAAATATATGGTGGAGACTGGTTGGGATCATAAAGCCCAATATATTTATTGTATGGTCtgtgt-tagccaggagtcttcagagaaacagaaccaataagataCA
TACAATAAATCAGAGGTCAGCAAGCTATAGGTTTT----TTAAACAGGACAAAAAATATACAACAGAGAAAATGTAGGACCAGAAAACCCAACATATTTATTATATGGGCTTTTTGTGgtcagggttctcctgtgaaacaggaccaataggatgta

3 SCAFFOLD1 3665 3845 chrX 44391563 44391740 + 7187
CCCTAAAAAGTCA-GTTTTTCA------AGAAGCATAAGCATAGTGTAAATGTAGGAGTTCATAGATCCATAGCAGGGAGAGCTGTTTAGCCTACTTATAGCTTATTTCCAGCTTATATCATCTGTTTGGGGCACGGTCATCCCTAGAGGCAGAGGAA-GAGATTTGGAATGAGGTTTTAGCATGATAT
TCCTGAAAATTTATATTTTTCACCAAGAAGAAACATAAACATCTTGCACA---AGGA---CATAAATCTATAGCTGGGGGTGCTGTT-AGTCTAGTTCTAGCATATTTCTAGCCTACATCATCTGTTTGGGGCATAATCATGTCTGGAAGAAAAGGAATGAGGTTTG----GGGATTTTAGCATGGTAT

17 SCAFFOLD2 22789 22919 chrX 44409117 44409239 - 5180
AGAATACACATCATAGTTATCATAGGGGAAT-GTTTAGGTGGCAGGATAAGGCATATTT--TTTTCTTTTCTCTGGTCTGTAAATTCTCTAACATAACTATATTGCTTTTAAATTTTAAATTGATTTTCAATTA
agaaaacacacc-cacttataatagtggatttgtccaggtggcaggactatacatctttgttttctttttttcttgtTTATAAATGTTCTAATATAACTATATTGCCtttaaa----------atttttaatta