+from unittest2 import TestCase
+from htsworkflow.submission.fastqname import FastqName
+
+class TestFastqName(TestCase):
+ def test_init_empty(self):
+ fq = FastqName()
+ self.assertEqual(fq.is_valid, False)
+
+ def test_init_single_filename(self):
+ fq = FastqName(filename="12345_AABBCCDDXX_c100_l1.fastq")
+ self.assertEqual(fq.lib_id, "12345")
+ self.assertEqual(fq['lib_id'], "12345")
+ self.assertEqual(fq.flowcell, "AABBCCDDXX")
+ self.assertEqual(fq['flowcell'], "AABBCCDDXX")
+ self.assertEqual(fq.cycle, "100")
+ self.assertEqual(fq['cycle'], "100")
+ self.assertEqual(fq.lane, "1")
+ self.assertEqual(fq['lane'], "1")
+ self.assertEqual(fq.is_paired, False)
+
+ def test_init_single_filename(self):
+ fq = FastqName(filename="12345_AABBCCDDXX_c100_l1_r2.fastq")
+ self.assertEqual(fq.lib_id, "12345")
+ self.assertEqual(fq['lib_id'], "12345")
+ self.assertEqual(fq.flowcell, "AABBCCDDXX")
+ self.assertEqual(fq['flowcell'], "AABBCCDDXX")
+ self.assertEqual(fq.cycle, "100")
+ self.assertEqual(fq['cycle'], "100")
+ self.assertEqual(fq.lane, "1")
+ self.assertEqual(fq['lane'], "1")
+ self.assertEqual(fq.read, "2")
+ self.assertEqual(fq['read'], "2")
+ self.assertEqual(fq.is_paired, True)
+
+ def test_init_bad_filename(self):
+ attribs = {'filename': 'asdf.bam'}
+ self.assertRaises(ValueError, FastqName, **attribs)
+
+ def test_init_single_attributes(self):
+ fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
+ cycle = "100", lane="1")
+ self.assertEqual(fq.is_valid, True)
+ self.assertEqual(fq.lib_id, "12345")
+ self.assertEqual(fq['lib_id'], "12345")
+ self.assertEqual(fq.flowcell, "AABBCCDDXX")
+ self.assertEqual(fq['flowcell'], "AABBCCDDXX")
+ self.assertEqual(fq.cycle, "100")
+ self.assertEqual(fq['cycle'], "100")
+ self.assertEqual(fq.lane, "1")
+ self.assertEqual(fq['lane'], "1")
+ self.assertEqual(fq.is_paired, False)
+ self.assertEqual(fq.filename, "12345_AABBCCDDXX_c100_l1.fastq")
+
+ def test_init_single_attributes_set_single(self):
+ fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
+ cycle = "100", lane="1", is_paired=False)
+ self.assertEqual(fq.is_valid, True)
+ self.assertEqual(fq.is_paired, False)
+
+ def test_init_single_attributes_set_paired(self):
+ fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
+ cycle = "100", lane="1", is_paired=True)
+ self.assertEqual(fq.is_valid, False)
+ self.assertEqual(fq.is_paired, True)
+
+ def test_init_paired_attributes(self):
+ fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
+ cycle = "100", lane="1", read="2")
+ self.assertEqual(fq.is_valid, True)
+ self.assertEqual(fq.lib_id, "12345")
+ self.assertEqual(fq['lib_id'], "12345")
+ self.assertEqual(fq.flowcell, "AABBCCDDXX")
+ self.assertEqual(fq['flowcell'], "AABBCCDDXX")
+ self.assertEqual(fq.cycle, "100")
+ self.assertEqual(fq['cycle'], "100")
+ self.assertEqual(fq.lane, "1")
+ self.assertEqual(fq['lane'], "1")
+ self.assertEqual(fq.read, "2")
+ self.assertEqual(fq['read'], "2")
+ self.assertEqual(fq.is_paired, True)
+ self.assertEqual(fq.filename, "12345_AABBCCDDXX_c100_l1_r2.fastq")
+
+ def test_init_paired_attributes_set_single(self):
+ fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
+ cycle = "100", lane="1", read="2", is_paired=False)
+ self.assertEqual(fq.is_valid, True)
+ self.assertEqual(fq.is_paired, False)
+
+ def test_init_paired_attributes_set_paired(self):
+ fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
+ cycle = "100", lane="1", read="2", is_paired=True)
+ self.assertEqual(fq.is_valid, True)
+ self.assertEqual(fq.is_paired, True)
+
+ def test_init_insufficient_attributes(self):
+ attribs = dict(lib_id="12345", flowcell="AABBCCDDXX")
+ fq = FastqName(**attribs)
+ self.assertEqual(fq.is_valid, False)
+
+
+def suite():
+ from unittest2 import TestSuite, defaultTestLoader
+ suite = TestSuite()
+ suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestFastqName))
+ return suite
+
+if __name__ == "__main__":
+ from unittest2 import main
+ main(defaultTest='suite')