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annotate tests/test_riboseqr.py @ 3:d7ce95ccf54f

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Change R data file format in xml wrappers (rda -> RData) Add test data, sample workflow. Updated README with instructions on testing.
author Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
date Wed, 22 Jul 2015 12:07:39 +0100
parents c34c364ce75d
children 423ad61697c4
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1 """riboSeqR Galaxy unit tests"""
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2 import unittest
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3 from riboseqr import utils
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6 class PrepareTestCase(unittest.TestCase):
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8 def test_process_args(self):
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9 """Test processing arguments. """
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10 # "ATG" -> c("ATG")
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11 rs = utils.process_args('ATG', ret_mode='charvector')
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12 self.assertEqual(rs, 'c("ATG")','Return string as a character vector.')
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13
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14 # stop codons "TAG,TAA,TGA" -> c("TAG", "TAA", "TGA"). Also
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15 # replicate names, seqnames.
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16 rs = utils.process_args('TAG,TAA,TGA', ret_mode='charvector')
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17 self.assertEqual(
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18 rs, "c('TAG', 'TAA', 'TGA')",
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19 'Return comma separated strings as a character vector.')
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20
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21 # "" -> None
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22 rs = utils.process_args('')
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23 self.assertIsNone(rs, 'Return empty string as None.')
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25 # "27,28" -> c(27, 28)
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26 rs = utils.process_args("27,28", ret_type='int', ret_mode='charvector')
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27 self.assertEqual(
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28 rs, "c(27, 28)", 'Return number strings as a character vector.')
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30 # "27,28" -> [27, 28]
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31 rs = utils.process_args("27,28", ret_type='int', ret_mode='list')
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32 self.assertEqual(rs, [27, 28], 'Return number strings as a list.')
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33
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34 # "0,2" -> list(0,2)
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35 rs = utils.process_args("0,2", ret_type='int', ret_mode='listvector')
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36 self.assertEqual(
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37 rs, "list(0, 2)", 'Return number strings as a list vector.')
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38
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39 # "50" -> 50
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40 rs = utils.process_args("50", ret_type='int')
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41 self.assertEqual(rs, 50, 'Return number string as a number.')
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42
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43 # "-200" -> -200
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44 rs = utils.process_args("-200", ret_type='int')
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45 self.assertEqual(rs, -200, 'Return number string as a number.')
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46
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47 # "TRUE" -> TRUE
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48 rs = utils.process_args("TRUE", ret_type='bool')
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49 self.assertEqual(rs, 'TRUE', 'Return bool string as bool.')
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51 # 'chlamy17,chlamy3' -> 'chlamy17,chlamy3' for ribo and rna names
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52 rs = utils.process_args('chlamy17,chlamy3')
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53 self.assertEqual(rs, 'chlamy17,chlamy3', 'Return csv string as string.')
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54
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55 # 'chlamy17.idx, chlamy3.idx' -> ['chlamy17.idx', 'chlamy3.idx']
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56 rs = utils.process_args('chlamy17.idx, chlamy3.idx', ret_mode='list')
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57 self.assertEqual(rs, ['chlamy17.idx', 'chlamy3.idx'],
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58 'Return files as a list.')