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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 89);
use_ok('Bio::Tools::Run::Alignment::Exonerate');
}
my $verbose = test_debug() || -1;
my $query= test_input_file("exonerate_cdna.fa");
my $target= test_input_file("exonerate_genomic.fa");
my $targetrev= test_input_file("exonerate_genomic_rev.fa");
my $run = Bio::Tools::Run::Alignment::Exonerate->new(-verbose => $verbose,
arguments=>'--model est2genome --bestn 1');
SKIP: {
test_skip(-requires_executable => $run, -tests => 88);
isa_ok $run, 'Bio::Tools::Run::Alignment::Exonerate';
ok $run->version;
my $searchio= $run->run($query,$target);
isa_ok $searchio, "Bio::SearchIO";
my @expect = ( [qw(29 268 4 242)],# target-start t-end query-start q-end
[qw(526 646 243 363)],
[qw(964 1056 364 456)],
[qw(1770 1923 457 610)],
[qw(2250 2479 611 840 )],
[qw(2565 2687 841 963)],
[qw(2769 3074 964 1279)] );
RESULT: while(my $result = $searchio->next_result){
while( my $hit = $result->next_hit ) {
# ok($hit->start('hit'), 29);
# ok($hit->end('hit'), 3074);
my $i = 0;
while( my $hsp = $hit->next_hsp ) {
is ($hsp->hit->strand, 1);
is ($hsp->query->strand, 1);
is ($hsp->hit->start,$expect[$i]->[0]);
is ($hsp->hit->end,$expect[$i]->[1]);
is ($hsp->query->start,$expect[$i]->[2]);
is ($hsp->query->end,$expect[$i]->[3]);
$i++;
if( $verbose > 0 ) {
warn("TARGET:", $hsp->hit->location->to_FTstring, "\n");
warn("QUERY: ",$hsp->query->location->to_FTstring, "\n");
}
}
last; # only show a single HIT
}
last;
}
$searchio= $run->run($query,$targetrev);
isa_ok $searchio,"Bio::SearchIO";
my @expectrev;
if ($run->version >= 2 ) { # latest 2.0.0 version
@expectrev = ( # target-start t-end query-start q-end
[qw(2834 3073 4 242)],
[qw(2456 2576 243 363)],
[qw(2046 2138 364 456)],
[qw(1179 1332 457 610)],
[qw(623 852 611 840)],
[qw(415 537 841 963)],
[qw(28 333 964 1279)]
);
} else { # version 1.4.0 presumably
@expectrev = ( # target-start t-end query-start q-end
[qw(28 333 964 1279)],
[qw(415 537 841 963)],
[qw(623 852 611 840)],
[qw(1179 1332 457 610)],
[qw(2046 2138 364 456)],
[qw(2456 2576 243 363)],
[qw(2834 3073 4 242)]
);
}
RESULT: while(my $result = $searchio->next_result){
while( my $hit = $result->next_hit ) {
my $i = 0;
while( my $hsp = $hit->next_hsp ) {
is ($hsp->hit->strand, -1);
is ($hsp->query->strand, 1);
is ($hsp->hit->start,$expectrev[$i]->[0]);
is ($hsp->hit->end,$expectrev[$i]->[1]);
is ($hsp->query->start,$expectrev[$i]->[2]);
is ($hsp->query->end,$expectrev[$i]->[3]);
$i++;
if( $verbose > 0 ) {
warn("TARGET:", $hsp->hit->location->to_FTstring, "\n");
warn("QUERY: ",$hsp->query->location->to_FTstring, "\n");
}
}
last; # only show a single HIT
}
last;
}
}