[Bioperl-l] XML -> Flat Query-Anchored & Identities

[simon andrews (BI)]

> -----Original Message-----
> From: Fanteï Caujolle Yan [mailto:Yan.Fantei at unice.fr]
> Sent: 06 August 2003 09:31
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] XML -> Flat Query-Anchored & Identities
> 
> 
> Hello all,
> 
> How to create a "Flat Query-Anchored with Identities" report from xml
> blast result (option -m7 of Blast) ?

Not exactly sure of the output format you want, but you probably want
to use the Bio::SearchIO module to parse your blast report.

#!/usr/bin/perl -w
use strict;
use Bio::SearchIO;

my $search = Bio::SearchIO -> new (-format => 'blastxml',
                                   -file => 'your_blast_file.xml');

# Assuming you only have one report in your file.
# You can put this in a loop for a multiple report file

my $report = Bio::SearchIO -> next_report();

while (my $hit = $report -> next_hit()){

  print "Found a hit to ", $hit->name; 
  print " which is ", $hit->description() , "\n";

  # Again you can put this bit in a loop if you want
  # details for individual hsps
  my $first_hsp = $hit -> next_hsp();

  print "Total length of hit was ", $hsp->length('total'),"bp \n";
  print "Total identity of hit was ", $hsp->frac_identical('total'),"% \n";	

}