fix GFF start position

daler · May 5, 2011 · c0163ce · c0163ce · brentp · May 5, 2011
1 parent 0348616
commit c0163ce
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diff --git a/pybedtools/cbedtools.pyx b/pybedtools/cbedtools.pyx
@@ -99,12 +99,16 @@ cdef class Interval:
             self._bed.fields[idx] = string(chrom)
 
     property start:
-        """ the start of the feature"""
+        """ the 0-based start of the feature"""
         def __get__(self):
             return self._bed.start
         def __set__(self, int start):
             self._bed.start = start
             idx = LOOKUPS[self.file_type]["start"]
+
+            # Non-BED files should have 1-based coords in fields
+            if self.file_type != 'bed': start += 1
+
             s = str(start)
             self._bed.fields[idx] = string(s)
 

diff --git a/pybedtools/test/test_cbedtools.py b/pybedtools/test/test_cbedtools.py
@@ -181,6 +181,35 @@ def setUp(self):
         self.i = Interval("chr1", start, end, strand)
         self.start, self.end, self.strand = start, end, strand
 
+    # Overwrite IntervalTest.testStart
+    def testStart(self):
+        ivf = IntervalFile(self.file)
+        iv = ivf.next()
+        orig_string = str(iv)
+
+        # 0-based.
+        orig_start = iv.start
+
+        # Setting .start always sets 0-based coord.
+        iv.start = orig_start
+
+        # But for GFF setting .start should also make the .fields[3] the GFF
+        # 1-based coord
+        assert iv.start == int(iv.fields[3])-1
+
+        second_string = str(iv)
+        second_start = iv.start
+        iv.start = second_start
+
+        # Check .start and .fields[3] internal consistency again
+        assert iv.start == int(iv.fields[3])-1
+
+        print '   orig:', '(start=%s)'%orig_start, orig_string
+        print ' second:', '(start=%s)'%second_start, second_string
+        print 'current:', '(start=%s)'%iv.start, str(iv)
+        self.assert_(orig_start == second_start == iv.start)
+        self.assert_(orig_string == second_string == str(iv))
+
 
 
 if __name__ == "__main__":