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# -*-Perl-*- Test Harness script for Bioperl
# $Id: FeatureIO.t 15112 2008-12-08 18:12:38Z sendu $
use strict;
use warnings;
use Bio::Root::Test;
use Bio::FeatureIO;
{
my @expected_features =
(
{
'seq_id' => 'C02HBa0072A04.1',
'primary_tag' => 'moderate_match',
'end' => '60548',
'start' => '60522'
},
{
'seq_id' => 'SL_FOS91h17_SP6_0',
'primary_tag' => 'strong_match',
'end' => '122',
'start' => '60'
},
{
'seq_id' => 'SL_FOS91h18_T7_0',
'primary_tag' => 'strong_match',
'end' => '102',
'start' => '35'
},
{
'seq_id' => 'SL_FOS91h18_T7_0',
'primary_tag' => 'moderate_match',
'end' => '103',
'start' => '76'
},
{
'seq_id' => 'SL_FOS91h18_T7_0',
'primary_tag' => 'weak_match',
'end' => '104',
'start' => '82'
},
{
'seq_id' => 'SL_FOS91h18_T7_0',
'primary_tag' => 'suspect_origin',
'end' => '34',
'start' => '1'
},
{
'seq_id' => 'SL_FOS91i01_SP6_0',
'primary_tag' => 'strong_match',
'end' => '110',
'start' => '46'
},
{
'seq_id' => 'SL_FOS91i01_SP6_0',
'primary_tag' => 'suspect_origin',
'end' => '45',
'start' => '1'
},
{
'seq_id' => 'SL_FOS92b12_T7_0',
'primary_tag' => 'strong_match',
'end' => '108',
'start' => '41'
},
{
'seq_id' => 'SL_FOS92b12_T7_0',
'primary_tag' => 'moderate_match',
'end' => '109',
'start' => '82'
},
{
'seq_id' => 'SL_FOS92b12_T7_0',
'primary_tag' => 'weak_match',
'end' => '110',
'start' => '88'
},
{
'seq_id' => 'SL_FOS92b12_T7_0',
'primary_tag' => 'weak_match',
'end' => '1329',
'start' => '1313'
},
{
'seq_id' => 'SL_FOS92b12_T7_0',
'primary_tag' => 'suspect_origin',
'end' => '40',
'start' => '1'
},
{
'seq_id' => 'SL_FOS92b12_T7_0',
'primary_tag' => 'suspect_origin',
'end' => '1334',
'start' => '1330'
}
);
my @vs_features;
my $vs_in = Bio::FeatureIO->new( -file => test_input_file('vecscreen_simple.test_output'),
-format => 'vecscreen_simple',
);
ok( $vs_in );
while(my $feat = $vs_in->next_feature) {
push @vs_features,$feat;
}
#convert the array of feature objects to something that can more easily be checked with is_deeply
@vs_features = map {
my $f = $_;
my $rec = { map {$_ => $f->$_()} qw/start end primary_tag seq_id/ };
} @vs_features;
is_deeply(\@vs_features,\@expected_features,'vecscreen_simple gets the correct features');
}
done_testing();
exit;
|
