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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
##
my $error;
use strict;
BEGIN {
# to handle systems with no installed Test module
# we include the t dir (where a copy of Test.pm is located)
# as a fallback
$error = 0;
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
use vars qw($TESTCOUNT);
$TESTCOUNT = 38;
plan tests => $TESTCOUNT;
}
use Bio::SearchIO;
use Bio::Root::IO;
my $pslparser = new Bio::SearchIO(-format => 'psl',
-file => Bio::Root::IO->catfile
(qw(t data sbay_c545-yeast.BLASTZ.PSL)));
my $result = $pslparser->next_result;
ok($result->query_name, 'I');
ok($result->query_length, 230203);
my $hit = $result->next_hit;
ok($hit->name, 'sbay_c545');
ok($hit->length, 28791);
my $hsp = $hit->next_hsp;
ok($hsp->query->start,139871);
ok($hsp->query->end,141473);
my $q_gapblocks = $hsp->gap_blocks('query');
ok(scalar @$q_gapblocks, 24);
ok($q_gapblocks->[0]->[1],45);
ok($q_gapblocks->[1]->[1],10);
ok($q_gapblocks->[1]->[0],139921);
$hsp = $hit->next_hsp;
$hsp = $hit->next_hsp;
ok($hsp->hit->start,27302);
ok($hsp->hit->end,27469);
ok($hsp->query->start, 123814);
ok($hsp->query->end, 123973);
ok($hsp->query->strand,-1);
$q_gapblocks = $hsp->gap_blocks('query');
ok(scalar @$q_gapblocks, 4);
ok($q_gapblocks->[0]->[1],116);
ok($q_gapblocks->[1]->[1],4);
ok($q_gapblocks->[1]->[0],123856);
#-----------------------------------
$pslparser = new Bio::SearchIO(-format => 'psl',
-file => Bio::Root::IO->catfile
(qw(t data blat.psLayout3)));
$result = $pslparser->next_result;
ok($result->query_name, 'sequence_10');
ok($result->query_length, 1775);
$hit = $result->next_hit;
ok($hit->name, 'sequence_10');
ok($hit->length, 1775);
$hsp = $hit->next_hsp;
ok($hsp->query->start,1);
ok($hsp->query->end,1776);
$q_gapblocks = $hsp->gap_blocks('query');
ok(scalar @$q_gapblocks, 1);
ok($q_gapblocks->[0]->[1],1775);
ok($q_gapblocks->[1]->[1],undef);
ok($q_gapblocks->[1]->[0],undef);
$hsp = $hit->next_hsp;
ok($hsp->hit->start,841);
ok($hsp->hit->end,1245);
ok($hsp->query->start, 841);
ok($hsp->query->end, 1245);
ok($hsp->query->strand,-1);
$q_gapblocks = $hsp->gap_blocks('query');
ok(scalar @$q_gapblocks, 4);
ok($q_gapblocks->[0]->[1],14);
ok($q_gapblocks->[1]->[1],21);
ok($q_gapblocks->[1]->[0],1152);
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