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use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 3);
use_ok('Bio::Tools::PrositeScan');
use_ok('Bio::SeqFeature::FeaturePair');
}
# Note: data generated by running
#
# ./ps_scan.pl --pfscan ./pfscan -d prosite.dat -o fasta \
# t/data/test.fasta > t/data/ps_scan/out.PrositeScan
#
# followed by a manual removal of some of the output to simplify the test.
subtest "Predictions" => sub {
my $factory = Bio::Tools::PrositeScan->new(
'-file' => test_input_file('ps_scan/out.PrositeScan'),
'-format' => 'fasta'
);
my $expected_matches = [
{ seq_id => 'roa1_drome', coords => [253, 256], psac => 'PS00001', subseq => 'NNSF' },
{ seq_id => 'roa1_drome', coords => [270, 273], psac => 'PS00001', subseq => 'NNSW' },
{ seq_id => 'roa2_drome', coords => [344, 349], psac => 'PS00008', subseq => 'GNNQGF' },
{ seq_id => 'roa2_drome', coords => [217, 355], psac => 'PS50321', subseq => re(qr/NR.{135}NN/) },
];
my $actual_matches = [];
while( my $match = $factory->next_prediction ) {
push @$actual_matches, {
seq_id => $match->seq_id,
coords => [ $match->start, $match->end ],
psac => $match->hseq_id,
subseq => $match->feature1->seq->seq,
};
}
cmp_deeply( $actual_matches, $expected_matches, 'Comparing parsed prediction input' );
};
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