[Bioperl-l] Generate a hsp from emboss format?

[Antony03]

Hi!
For example, with this code I can easily modify only one string:

 #! /usr/bin/perl -w
 
# use strict;
 use Bio::SeqIO;
 use Bio::Tools::Run::StandAloneBlast;
 use Bio::Seq;
 use warnings;
 
###########################################################################################################
# Usage information
die "Usage: $0 <sequence 1> <sequence 2> <BLAST algorithme> <minimum % of
identity>\n", if (@ARGV != 4);
 my ($infile1,$infile2,$algo,$identity) = @ARGV;
##########################################################################################################


 my $query1_in  = Bio::SeqIO->newFh ( -file   => "$infile1",
  				    -format => 'fasta' );
 my $query1 = <$query1_in>; 
 my $query2_in  = Bio::SeqIO->newFh ( -file   => "$infile2", 
  				      -format => 'fasta' );
 my $query2 = <$query2_in>; 
 
 my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  => "$algo");
 my $report = $factory->bl2seq($query1, $query2);

############################################################################################################
 while (my $result = $report->next_result) {  # while 1
    print "Query: ".$result->query_name."\n\n";
    while (my $hit = $result->next_hit) {     # while 2
 	while (my $hsp = $hit->next_hsp) {    # while 3
 
if ( $hsp->percent_identity >= "$identity" ) 

	{ # start of if


	print $hsp->algorithm, ": Identity ", 100*$hsp->frac_identical, "\%, Rank
", $hsp->rank, " (evalue:", $hsp->evalue, ")\n";
	print "\t", $hsp->query_string;
	print "\n";
	print "\t", $hsp->homology_string;
	print "\n";
	print "\t", $hsp->hit_string;
	print "\n\n";
		
}
 	} # end of while 3
    print "\n";
    }	# end of while 2
 }	# end of while 3

This is why I want to have this format. Is this possible?
Thanks!


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