Imported Upstream version 0.2.4

[tabix.git] / python / test.py

diff --git a/python/test.py b/python/test.py
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+#
+# The MIT License
+#
+# Copyright (c) 2011 Seoul National University.
+#
+# Permission is hereby granted, free of charge, to any person obtaining
+# a copy of this software and associated documentation files (the
+# "Software"), to deal in the Software without restriction, including
+# without limitation the rights to use, copy, modify, merge, publish,
+# distribute, sublicense, and/or sell copies of the Software, and to
+# permit persons to whom the Software is furnished to do so, subject to
+# the following conditions:
+#
+# The above copyright notice and this permission notice shall be
+# included in all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+#
+# Contact: Hyeshik Chang <hyeshik@snu.ac.kr>
+
+import unittest
+import random
+import gzip
+import tabix
+
+EXAMPLEFILE = '../example.gtf.gz'
+
+def load_example_regions(path):
+    alldata = []
+    for line in gzip.GzipFile(EXAMPLEFILE):
+        fields = line.decode('ascii')[:-1].split('\t')
+        seqid = fields[0]
+        begin = int(fields[3])
+        end = int(fields[4])
+        alldata.append((seqid, begin, end, fields[:7]))
+
+    return alldata
+
+def does_overlap(A, B, C, D):
+    return (A <= D <= B) or (C <= B <= D)
+
+def sample_test_dataset(regions, ntests):
+    seqids = [seqid for seqid, _, _, _ in regions]
+    lowerbound = max(0, min(begin for _, begin, _, _ in regions) - 1000)
+    upperbound = max(end for _, _, end, _ in regions) + 1000
+
+    tests = []
+    for i in range(ntests):
+        seqid = random.choice(seqids)
+        low = random.randrange(lowerbound, upperbound)
+        high = random.randrange(low, upperbound)
+
+        # for 1-based both-end inclusive intervals
+        matches = [info for seq, begin, end, info in regions
+                   if seqid == seq and does_overlap(begin, end, low, high)]
+
+        tests.append((seqid, low, high, matches))
+
+    return tests
+
+def tbresult2excerpt(tbmatches):
+    return [fields[:7] for fields in tbmatches]
+
+class TabixTest(unittest.TestCase):
+    regions = load_example_regions(EXAMPLEFILE)
+    testset = sample_test_dataset(regions, 500)
+
+    def setUp(self):
+        self.tb = tabix.Tabix(EXAMPLEFILE)
+
+    def testQuery(self):
+        for seqid, low, high, matches in self.testset:
+            tbresult = tbresult2excerpt(self.tb.query(seqid, low, high))
+            self.assertEqual(tbresult, matches)
+
+    def testQueryS(self):
+        for seqid, low, high, matches in self.testset:
+            tbresult = tbresult2excerpt(self.tb.querys('%s:%d-%d' %
+                                                       (seqid, low, high)))
+            self.assertEqual(tbresult, matches)
+
+
+if __name__ == '__main__':
+    unittest.main()