diff test/test_combine_output.py @ 0:9d5f4f5f764b

Initial commit to toolshed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test/test_combine_output.py	Thu Jan 16 13:10:00 2014 +0100
@@ -0,0 +1,106 @@
+'''
+Created on Mar 27, 2012
+
+@author: marcelk
+'''
+from GCMS import combine_output
+from pkg_resources import resource_filename  # @UnresolvedImport # pylint: disable=E0611
+import os
+import shutil
+import tempfile
+import unittest
+
+
+class Test(unittest.TestCase):
+    '''
+    Tests for the 'combine_output' Galaxy tool
+    '''
+
+    def setUp(self):
+        self.rf_output = resource_filename(__name__, "data/RankFilter.txt")
+        self.cl_output = resource_filename(__name__, "data/CasLookup.txt")
+
+    def test_process_data(self):
+        '''
+        Tests the processing of the RankFilter and CasLookup files into dictionaries
+        '''
+        rfdata = combine_output._process_data(self.rf_output)
+        cldata = combine_output._process_data(self.cl_output)
+        self.assertEqual(set([' 18457-04-0', ' 55133-95-4', ' 58-08-2', ' 112-34-5']), set(rfdata['CAS']))
+        self.assertEqual(set(['C58082', 'C18457040', 'C55133954', 'C112345']), set(cldata['CAS']))
+
+    def test_add_hit(self):
+        '''
+        Tests the combination of two records from both the RankFilter- and CasLookup-tools
+        '''
+        rfdata = combine_output._process_data(self.rf_output)
+        cldata = combine_output._process_data(self.cl_output)
+        index = 0
+        rf_record = dict(zip(rfdata.keys(), [rfdata[key][index] for key in rfdata.keys()]))
+        cl_record = dict(zip(cldata.keys(), [cldata[key][index] for key in cldata.keys()]))
+
+        hit = combine_output._add_hit(rf_record, cl_record)
+        self.assertEqual(len(hit), 27)
+
+        # Pass empty record, should fail combination
+        self.assertRaises(KeyError, combine_output._add_hit, rf_record, {})
+
+    def test_merge_data(self):
+        '''
+        Tests the merging of the RankFilter and CasLookup data
+        '''
+        rfdata = combine_output._process_data(self.rf_output)
+        cldata = combine_output._process_data(self.cl_output)
+        merged, _ = combine_output._merge_data(rfdata, cldata)
+        centrotypes = _get_centrotypes(merged)
+        self.failUnless(all(centrotype in centrotypes for centrotype in ('2716','12723', '3403', '12710')))
+
+def _get_centrotypes(merged):
+    '''
+    returns centrotype codes found in merged set
+    '''
+    result = []
+    for item_idx in xrange(len(merged)):
+        item = merged[item_idx]
+        centrotype = item[0][0]
+        result.append(centrotype) 
+
+    return result 
+
+    def test_remove_formula(self):
+        '''
+        Tests the removal of the Formula from the 'Name' field (RankFilter output)
+        '''
+        name = "Caffeine C8H10N4O2"
+        compound_name, compound_formula = combine_output._remove_formula(name)
+        self.assertEqual(compound_name, 'Caffeine')
+        self.assertEqual(compound_formula, 'C8H10N4O2')
+        name = "Ethanol C2H6O"
+        compound_name, compound_formula = combine_output._remove_formula(name)
+        self.assertEqual(compound_name, 'Ethanol')
+        self.assertEqual(compound_formula, 'C2H6O')
+        # No formula to remove
+        name = "Butanoic acid, 4-[(trimethylsilyl)oxy]-, trimethylsilyl ester"
+        compound_name, compound_formula = combine_output._remove_formula(name)
+        self.assertEqual(compound_name, name)
+        self.assertEqual(compound_formula, False)
+
+    def test_save_data(self):
+        '''
+        Tests the creation of the output tabular files (no content testing)
+        '''
+        temp_folder = tempfile.mkdtemp(prefix='gcms_combine_output_')
+        saved_single_data = '{0}/{1}'.format(temp_folder, 'output_single.tsv')
+        saved_multi_data = '{0}/{1}'.format(temp_folder, 'output_multi.tsv')
+        rfdata = combine_output._process_data(self.rf_output)
+        cldata = combine_output._process_data(self.cl_output)
+        merged, nhits = combine_output._merge_data(rfdata, cldata)
+        combine_output._save_data(merged, nhits, saved_single_data, saved_multi_data)
+        self.failUnless(os.path.exists(saved_single_data))
+        self.failUnless(os.path.exists(saved_multi_data))
+        shutil.rmtree(temp_folder)
+
+
+if __name__ == "__main__":
+    #import sys;sys.argv = ['', 'Test.testName']
+    unittest.main()