From f28aa63fd2e4d086f35e9d02eb235acb10765dab Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Fri, 14 Apr 2017 01:12:02 -0500
Subject: [PATCH] Add a test for PrositeScan

---
 t/Tools/PrositeScan.t          | 44 ++++++++++++++++++++++++++++++++++++++++++
 t/data/ps_scan/out.PrositeScan | 10 ++++++++++
 2 files changed, 54 insertions(+)
 create mode 100644 t/Tools/PrositeScan.t
 create mode 100644 t/data/ps_scan/out.PrositeScan

diff --git a/t/Tools/PrositeScan.t b/t/Tools/PrositeScan.t
new file mode 100644
index 000000000..bd983c598
--- /dev/null
+++ b/t/Tools/PrositeScan.t
@@ -0,0 +1,44 @@
+use strict;
+
+BEGIN {
+    use lib '.';
+    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' );
+};
diff --git a/t/data/ps_scan/out.PrositeScan b/t/data/ps_scan/out.PrositeScan
new file mode 100644
index 000000000..5740f086d
--- /dev/null
+++ b/t/data/ps_scan/out.PrositeScan
@@ -0,0 +1,10 @@
+>roa1_drome/253-256 : PS00001 ASN_GLYCOSYLATION 
+NNSF
+>roa1_drome/270-273 : PS00001 ASN_GLYCOSYLATION 
+NNSW
+>roa2_drome/344-349 : PS00008 MYRISTYL 
+GNNQGF
+>roa2_drome/217-355 : PS50321 ASN_RICH L=0 
+NRGNMGGGNYGNQNGGGNWNNGGNNWGNNRGNDNWGNNSFGGGGGGGGGYGGGNNSWGNN
+NPWDNGNGGGNFGGGGNNWNGGNDFGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAG
+GGNQGNYGNNQGFNNGGNN
-- 
2.11.4.GIT