Position converter detects incorrect order in ranges

This fixes Trac bug #95.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@524 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

mutalyzer/mapping.py

@@ -431,11 +431,16 @@ class Converter(object) :
         else :
             change = r_change
 
-        if M.start_g != M.end_g :
-            if self.dbFields["orientation"] == '+' :
-                var_in_g = "g.%s_%s%s" % (M.start_g, M.end_g, change)
-            else :
-                var_in_g = "g.%s_%s%s" % (M.end_g, M.start_g, change)
+        if M.start_g != M.end_g:
+            if self.dbFields["orientation"] == '-':
+                last_g, first_g = M.start_g, M.end_g
+            else:
+                first_g, last_g = M.start_g, M.end_g
+            if last_g < first_g:
+                self.__output.addMessage(__file__, 3, 'ERANGE', 'End position '
+                                         'is smaller than the begin position.')
+                return None
+            var_in_g = "g.%s_%s%s" % (first_g, last_g, change)
         #if
         else :
             var_in_g = "g.%s%s" % (M.start_g, change)
@@ -556,6 +561,11 @@ class Converter(object) :
         else :
             loc2 = loc
 
+        if loc2 < loc:
+            self.__output.addMessage(__file__, 3, 'ERANGE', 'End position is '
+                                     'smaller than the begin position.')
+            return None
+
         if gene:
             transcripts = self.__database.get_TranscriptsByGeneName(gene)
         else:

tests/test_mapping.py

@@ -94,3 +94,54 @@ class TestConverter():
         assert 'NM_002241.3:c.-27340-7_-27332del16' not in coding
         assert 'NM_002241.4:c.1-7_9del16' in coding
         assert 'NM_002241.3:c.1-7_9del16' in coding
+
+    def test_range_order_forward_correct(self):
+        """
+        Just a normal position converter call, both directions.  See Trac #95.
+        """
+        converter = self._converter('hg19')
+        genomic = converter.c2chrom('NM_003002.2:c.-1_274del')
+        assert_equal(genomic, 'NC_000011.9:g.111957631_111959695del')
+        coding = converter.chrom2c(genomic, 'list')
+        assert 'NM_003002.2:c.-1_274del' in coding
+
+    def test_range_order_forward_incorrect_c2chrom(self):
+        """
+        Incorrect order of a range on the forward strand. See Trac #95.
+        """
+        converter = self._converter('hg19')
+        genomic = converter.c2chrom('NM_003002.2:c.274_-1del')
+        assert_equal(genomic, None)
+        erange = self.output.getMessagesWithErrorCode('ERANGE')
+        assert_equal(len(erange), 1)
+
+    def test_range_order_reverse_correct(self):
+        """
+        Just a normal position converter call on the reverse strand, both
+        directions. See Trac #95.
+        """
+        converter = self._converter('hg19')
+        genomic = converter.c2chrom('NM_001162505.1:c.-1_40del')
+        assert_equal(genomic, 'NC_000020.10:g.48770135_48770175del')
+        coding = converter.chrom2c(genomic, 'list')
+        assert 'NM_001162505.1:c.-1_40del' in coding
+
+    def test_range_order_reverse_incorrect_c2chrom(self):
+        """
+        Incorrect order of a range on the reverse strand. See Trac #95.
+        """
+        converter = self._converter('hg19')
+        genomic = converter.c2chrom('NM_001162505.1:c.40_-1del')
+        assert_equal(genomic, None)
+        erange = self.output.getMessagesWithErrorCode('ERANGE')
+        assert_equal(len(erange), 1)
+
+    def test_range_order_incorrect_chrom2c(self):
+        """
+        Incorrect order of a chromosomal range. See Trac #95.
+        """
+        converter = self._converter('hg19')
+        coding = converter.chrom2c('NC_000011.9:g.111959695_111957631del', 'list')
+        assert_equal(coding, None)
+        erange = self.output.getMessagesWithErrorCode('ERANGE')
+        assert_equal(len(erange), 1)