Fixed bug in tx2genome() stranded handling

tleonardi · Feb 21, 2019 · c968072 · c968072
1 parent b43a17c
commit c968072
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Showing 2 changed files with 12 additions and 1 deletion.
diff --git a/bedparse/bedline.py b/bedparse/bedline.py
@@ -306,6 +306,9 @@ def tx2genome(self, coord, stranded=False):
         if not isinstance(coord, int):
             raise BEDexception("coord must be of type integer")
 
+        if stranded and not self.stranded:
+            raise BEDexception("The standed option only makes sense for stranded transcripts")
+
         # If the bed record if not type 12 set exStarts
         # and exLens to the whole transcript
         if self.bedType < 12:
@@ -317,7 +320,7 @@ def tx2genome(self, coord, stranded=False):
             exLens = [ int(i) for i in self.exLengths.split(',')if i!='' ]
             nEx=self.nEx
 
-        if stranded:
+        if stranded and self.strand == "-":
             coord = sum(exLens)-coord-1
 
         # Throw an exception is the coordinate is invalid

diff --git a/tests/tests.py b/tests/tests.py
@@ -165,6 +165,14 @@ class KnownValues(unittest.TestCase):
                     # Transcript
                     ['chr1', 1000, 2000, 'Tx1', '0', '+', 1000, 1000, 0, 1, '1000,', '0,'],
                     # Tuple of tuples (txCoord, GenomeCoord)
+                    ((0, 1000), (500, 1500), (999, 1999)),
+                    # Tuple of txCoord that should throw exception
+                    (-10, -100, "a", 0.7, 2000, 10000)
+                ),
+                (
+                    # Transcript
+                    ['chr1', 1000, 2000, 'Tx1', '0', '-', 1000, 1000, 0, 1, '1000,', '0,'],
+                    # Tuple of tuples (txCoord, GenomeCoord)
                     ((0, 1999), (500, 1499), (999, 1000)),
                     # Tuple of txCoord that should throw exception
                     (-10, -100, "a", 0.7, 2000, 10000)