diff tests/test_riboseqr.py @ 0:c34c364ce75d

First commit

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tests/test_riboseqr.py	Tue Jul 21 14:48:39 2015 +0100
@@ -0,0 +1,58 @@
+"""riboSeqR Galaxy unit tests"""
+import unittest
+from riboseqr import utils
+
+
+class PrepareTestCase(unittest.TestCase):
+
+    def test_process_args(self):
+        """Test processing arguments. """
+        # "ATG" -> c("ATG")
+        rs = utils.process_args('ATG', ret_mode='charvector')
+        self.assertEqual(rs, 'c("ATG")','Return string as a character vector.')
+
+        # stop codons "TAG,TAA,TGA" -> c("TAG", "TAA", "TGA"). Also
+        # replicate names, seqnames.
+        rs = utils.process_args('TAG,TAA,TGA', ret_mode='charvector')
+        self.assertEqual(
+            rs, "c('TAG', 'TAA', 'TGA')",
+            'Return comma separated strings as a character vector.')
+
+        # "" -> None
+        rs = utils.process_args('')
+        self.assertIsNone(rs, 'Return empty string as None.')
+
+        # "27,28" -> c(27, 28)
+        rs = utils.process_args("27,28", ret_type='int', ret_mode='charvector')
+        self.assertEqual(
+            rs, "c(27, 28)", 'Return number strings as a character vector.')
+
+        # "27,28" -> [27, 28]
+        rs = utils.process_args("27,28", ret_type='int', ret_mode='list')
+        self.assertEqual(rs, [27, 28], 'Return number strings as a list.')
+
+        # "0,2" -> list(0,2)
+        rs = utils.process_args("0,2", ret_type='int', ret_mode='listvector')
+        self.assertEqual(
+            rs, "list(0, 2)", 'Return number strings as a list vector.')
+
+        # "50" -> 50
+        rs = utils.process_args("50", ret_type='int')
+        self.assertEqual(rs, 50, 'Return number string as a number.')
+
+        # "-200" -> -200
+        rs = utils.process_args("-200", ret_type='int')
+        self.assertEqual(rs, -200, 'Return number string as a number.')
+
+        # "TRUE" -> TRUE
+        rs = utils.process_args("TRUE", ret_type='bool')
+        self.assertEqual(rs, 'TRUE', 'Return bool string as bool.')
+
+        # 'chlamy17,chlamy3' -> 'chlamy17,chlamy3' for ribo and rna names
+        rs = utils.process_args('chlamy17,chlamy3')
+        self.assertEqual(rs, 'chlamy17,chlamy3', 'Return csv string as string.')
+
+        # 'chlamy17.idx, chlamy3.idx' -> ['chlamy17.idx', 'chlamy3.idx']
+        rs = utils.process_args('chlamy17.idx, chlamy3.idx', ret_mode='list')
+        self.assertEqual(rs, ['chlamy17.idx', 'chlamy3.idx'],
+                         'Return files as a list.')