1# -*-Perl-*- Test Harness script for Bioperl 2# $Id: SearchIO_megablast.t 14995 2008-11-16 06:20:00Z cjfields $ 3 4use strict; 5 6BEGIN { 7 use Bio::Root::Test; 8 9 test_begin(-tests => 31); 10 11 use_ok('Bio::SearchIO'); 12} 13 14my ($searchio, $result, $hit, $hsp); 15 16# this is megablast output type 0 17my $in = Bio::SearchIO->new(-file => test_input_file('503384.MEGABLAST.0'), 18 -report_format => 0, 19 -format => 'megablast'); 20my $r = $in->next_result; 21my @dcompare = ( 22 ['Contig634', 7620, 7941, 1, 1, 321, -1], 23 ['Contig1853', 6406, 6620, 1, 1691, 1905, 1], 24 ['Contig3700', 8723,9434, 1, 4083, 4794, -1], 25 ['Contig3997', 1282, 1704, 1, 1546, 1968,-1 ], 26 ); 27 28is($r->query_name, '503384'); 29 30while( my $hit = $r->next_hit ) { 31 my $d = shift @dcompare; 32 is($hit->name, shift @$d); 33 my $hsp = $hit->next_hsp; 34 is($hsp->query->start, shift @$d); 35 is($hsp->query->end, shift @$d); 36 is($hsp->query->strand, shift @$d); 37 is($hsp->hit->start, shift @$d); 38 is($hsp->hit->end, shift @$d); 39 is($hsp->hit->strand, shift @$d); 40} 41is(@dcompare, 0); 42 43