Python create_from_rsat_feature_names Examples

Example #1

 def test_create_from_rsat_feature_names_with_transform(self):
     """test the creation from RSAT feature names using a key transformer"""
     thes = thesaurus.create_from_rsat_feature_names(
         MockRsatFeatureNameFile(), [lambda x: [x, x.rstrip('m')]])
     self.assertEquals('NAME1', thes['PRIME1'])
     self.assertEquals('NAME1', thes['ALT1'])
     self.assertEquals('NAME2', thes['PRIME2'])
     self.assertEquals('NAME2', thes['VNG2664G'])

Example #2

File: thesaurus_test.py Project: baliga-lab/cmonkey2

 def test_create_from_rsat_feature_names_with_transform(self):
     """test the creation from RSAT feature names using a key transformer"""
     thes = thesaurus.create_from_rsat_feature_names(
         MockRsatFeatureNameFile(), [lambda x: [x, x.rstrip('m')]])
     self.assertEquals('NAME1', thes['PRIME1'])
     self.assertEquals('NAME1', thes['ALT1'])
     self.assertEquals('NAME2', thes['PRIME2'])
     self.assertEquals('NAME2', thes['VNG2664G'])

Example #3

 def test_create_from_rsat_feature_names_no_transform(self):
     """test the creation from RSAT feature names file"""
     thes = thesaurus.create_from_rsat_feature_names(
         MockRsatFeatureNameFile())
     self.assertEquals('NAME1', thes['PRIME1'])
     self.assertEquals('NAME1', thes['ALT1'])
     self.assertEquals('NAME2', thes['PRIME2'])
     self.assertEquals('NAME2', thes['VNG2664Gm'])

Example #4

File: thesaurus_test.py Project: baliga-lab/cmonkey2

 def test_create_from_rsat_feature_names_no_transform(self):
     """test the creation from RSAT feature names file"""
     thes = thesaurus.create_from_rsat_feature_names(
         MockRsatFeatureNameFile())
     self.assertEquals('NAME1', thes['PRIME1'])
     self.assertEquals('NAME1', thes['ALT1'])
     self.assertEquals('NAME2', thes['PRIME2'])
     self.assertEquals('NAME2', thes['VNG2664Gm'])

Example #5

File: organism.py Project: baliga-lab/cmonkey2

 def thesaurus(self):
     """reads the thesaurus from a feature_names file. The thesaurus
     is also cached, because it is used many times
     """
     if not self.__synonyms:
         feature_names_dfile = util.dfile_from_text(self.__rsat_info.get_feature_names(), comment="--")
         self.__synonyms = thesaurus.create_from_rsat_feature_names(
             feature_names_dfile, [thesaurus.strip_vng_modification]
         )
     return self.__synonyms

Example #6

 def thesaurus(self):
     """reads the thesaurus from a feature_names file. The thesaurus
     is also cached, because it is used many times
     """
     if not self.__synonyms:
         feature_names_dfile = util.dfile_from_text(
             self.__rsat_info.get_feature_names(), comment='--')
         self.__synonyms = thesaurus.create_from_rsat_feature_names(
             feature_names_dfile, [thesaurus.strip_vng_modification])
     return self.__synonyms

Example #7

File: operon_nw_test.py Project: uweschmitt/cmonkey2

 def __make_organism(self):
     """makes a mock organism with almost real data"""
     features = {}
     dfile = util.read_dfile('testdata/Halobacterium_sp_features',
                             comment='--')
     for line in dfile.lines:
         features[line[0]] = st.Feature(
             line[0], line[1], line[2],
             st.Location(line[3], int(line[4]), int(line[5]),
                         line[6] == 'R'))
     tfile = util.read_dfile('testdata/Halobacterium_sp_feature_names',
                             comment='--')
     synonyms = th.create_from_rsat_feature_names(tfile)
     return MockOrganismWithSynonyms('64091', features, synonyms)

Example #8

File: operon_nw_test.py Project: baliga-lab/cmonkey2

 def __make_organism(self):
     """makes a mock organism with almost real data"""
     features = {}
     dfile = util.read_dfile('testdata/Halobacterium_sp_features',
                             comment='--')
     for line in dfile.lines:
         features[line[0]] = st.Feature(line[0], line[1], line[2],
                                        st.Location(line[3],
                                                    int(line[4]),
                                                    int(line[5]),
                                                    line[6] == 'R'))
     tfile = util.read_dfile(
         'testdata/Halobacterium_sp_feature_names', comment='--')
     synonyms = th.create_from_rsat_feature_names(tfile)
     return MockOrganismWithSynonyms('64091', features, synonyms)