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# -*-Perl-*- Test Harness script for Bioperl
# $Id: gmap_f9.t 14995 2008-11-16 06:20:00Z cjfields $
use strict;
use warnings;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 54);
use_ok('Bio::SearchIO');
}
my $searchio =
Bio::SearchIO->new(-format => 'gmap_f9',
-file => test_input_file('gmap_f9.txt'));
my $result = $searchio->next_result;
isa_ok($result, 'Bio::Search::Result::GenericResult', 'Did we get a Result?');
is($result->num_hits(), 1, 'Did we get the expected number of hits?');
is($result->algorithm(), 'gmap', 'Did we get the expected algorithm?');
is($result->query_name(), 'NM_004448', 'Did we get the expected query_name?');
my $hit = $result->next_hit;
isa_ok($hit, 'Bio::Search::Hit::GenericHit', 'Did we get a Hit?');
_check_hit($hit, {name => '17',
length => 4624,
num_hsps => 27,
query_length => 4623
} );
my $hsp = $hit->next_hsp;
_check_hsp($hsp, {algorithm => 'GMAP',
query_gaps => 1,
hit_gaps => 0,
query_length => 310,
hit_length => 311,
qseq => 'GGAGGAGGTGGAGGAGGAGG', # first 20 bases
hseq => 'GGAGGAGGTGGAGGAGGAGG', # ditto
query => {start => 1,
end => 310,
strand => 1},
hit => {start => 35109780,
end => 35110090,
strand => 1},
homology_string => 'GGAGGAGGTGGAGGAGGAGG',
seq_inds_query_gap => [(61)]
} );
my $searchio_rev =
Bio::SearchIO->new(-format => 'gmap_f9',
-file => test_input_file('gmap_f9-reverse-strand.txt'));
my $result_rev = $searchio_rev->next_result;
isa_ok($result_rev,
'Bio::Search::Result::GenericResult', 'Did we get a Result?');
is($result_rev->num_hits(), 1, 'Did we get the expected number of hits?');
is($result_rev->algorithm(), 'gmap', 'Did we get the expected algorithm?');
is($result_rev->query_name(),
'NM_004448', 'Did we get the expected query_name?');
$hit = $result_rev->next_hit;
_check_hit($hit, {name => '17',
length => 4624,
num_hsps => 27,
query_length => 4623
} );
$hsp = $hit->next_hsp;
_check_hsp($hsp, {algorithm => 'GMAP',
query_gaps => 0,
hit_gaps => 0,
query_length => 974,
hit_length => 974,
qseq => 'TAGCTGTTTTCCAAAATATA', # first 20 bases
hseq => 'TAGCTGTTTTCCAAAATATA', # ditto
query => {start => 1,
end => 974,
strand => 1},
hit => {start => 35137468,
end => 35138441,
strand => -1},
homology_string => 'TAGCTGTTTTCCAAAATATA',
seq_inds_query_gap => [()]
} );
$searchio = Bio::SearchIO->new(-format => 'gmap_f9',
-file => test_input_file('gmap_f9-multiple_results.txt'));
my $result_count = 0;
while (my $result = $searchio->next_result) {
$result_count++;
}
is($result_count, 58, "Can we loop over multiple results properly (expecting 58)?");
# bug 3021
$searchio = Bio::SearchIO->new(-format => 'gmap_f9',
-file => test_input_file('bug3021.gmap'));
$result = $searchio->next_result;
is($result->query_name, 'NM_004448', 'simple query_name now caught, bug 3021');
exit(0);
sub _check_hit {
my ($hit, $info) = @_;
isa_ok($hit, 'Bio::Search::Hit::HitI');
is($hit->name, $info->{name}, 'Check the name');
is($hit->length, $info->{length}, 'Check the hit length');
is($hit->num_hsps, $info->{num_hsps}, 'Check the number of hsps');
is($hit->query_length, $info->{query_length}, 'Check the query length');
}
sub _check_hsp {
my($hsp, $info) = @_;
isa_ok($hsp, 'Bio::Search::HSP::HSPI');
is($hsp->algorithm, $info->{algorithm}, 'Check the algorithm');
is($hsp->gaps('query'), $info->{query_gaps}, 'Count gaps in the query');
is($hsp->gaps('hit'), $info->{hit_gaps}, 'Count gaps in the hit');
is($hsp->length('query'), $info->{query_length}, 'Length of the query');
is($hsp->length('hit'), $info->{hit_length}, 'Length of the hit');
is(substr($hsp->query_string, 0, 20), $info->{qseq}, 'Query sequence');
is(substr($hsp->hit_string, 0, 20), $info->{hseq}, 'Hit sequence');
is($hsp->query->start, $info->{query}->{start}, "Check query start");
is($hsp->query->end, $info->{query}->{end}, "Check query end");
is($hsp->query->strand, $info->{query}->{strand}, "Check query end");
is(substr($hsp->homology_string, 0, 20), $info->{homology_string}, 'Check the homology string');
is_deeply([$hsp->seq_inds('query', 'gap')], $info->{seq_inds_query_gap}, 'Check seq_inds');
is($hsp->hit->start, $info->{hit}->{start}, "Check hit start");
is($hsp->hit->end, $info->{hit}->{end}, "Check hit end");
is($hsp->hit->strand, $info->{hit}->{strand}, "Check hit end");
}
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