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# written by Juguang Xiao
use strict;
BEGIN {
use lib 't';
use Test;
plan tests => 3;
}
END { }
use Bio::SearchIO;
my $searchio = new Bio::SearchIO(
-format => 'blast',
-file => 't/data/blast.report'
);
my @hsps = ();
while(my $result = $searchio->next_result){
while(my $hit = $result->next_hit){
while(my $hsp = $hit->next_hsp){
push @hsps, $hsp;
}
}
}
my $first_hsp = shift @hsps;
my $first_hsp_cigar_string = '504M';
ok $first_hsp->cigar_string, $first_hsp_cigar_string;
ok $first_hsp->cigar_string, $first_hsp_cigar_string; # fetch from hash
my $second_hsp = $hsps[0];
my $second_hsp_cigar_string = '29M18I22M11I20MD33M4I22M3I25M5I21MI33MD14M';
ok $second_hsp->cigar_string, $second_hsp_cigar_string;
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