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

[Jason Stajich]

There's no midline/homology line in the axt format so there is no way to know
which columns are identical so I don't see how it can work.

-jason
-- 
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/


Quoting Alynne Chiromatzo <chiromatzo at gmail.com>:

> 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
> 
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