Merge pull request #55 from standage/range_funcs

Simpler range and point overlap queries

CHANGELOG.md

@@ -2,6 +2,11 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [0.3.0] - 2017-02-02
+### Added
+- New convenience functions in the `Range` and `Feature` classes for range and
+  point overlap queries.
+
 ## [0.2.0] - 2017-01-18
 ### Added
 - An index class for efficient in-memory access of sequence features.

tag/feature.py

@@ -28,6 +28,8 @@ class Feature(object):
     'gene'
     >>> feature.start, feature.end
     (999, 7500)
+    >>> feature.contains_point(2044)
+    True
     >>> feature.score is None
     True
     >>> feature.strand
@@ -465,3 +467,11 @@ def cdslen(self):
             return None
 
         return sum([len(c) for c in self.children if c.type == 'CDS'])
+
+    def contains(self, rng):
+        """Report whether this feature contains the specified range."""
+        return self._range.contains(rng)
+
+    def contains_point(self, point):
+        """Report whether this feature contains the specified point."""
+        return self._range.contains_point(point)

tag/range.py

@@ -21,6 +21,10 @@ class Range(object):
     [0, 1000)
     >>> len(rng)
     1000
+    >>> rng.contains(Range(10, 20))
+    True
+    >>> rng.contains_point(2345)
+    False
     >>> rng.start = 500
     >>> rng.start
     500
@@ -136,9 +140,11 @@ def overlap(self, other):
 
     def contains(self, other):
         """Determine whether this range contains another."""
-        if self._start <= other.start and self._end >= other.end:
-            return True
-        return False
+        return self._start <= other.start and self._end >= other.end
+
+    def contains_point(self, point):
+        """Determine whether this range contains the specified point."""
+        return self._start <= point and self._end >= point
 
     def within(self, other):
         """Determine whether this range is contained within another."""

tests/test_feature.py

@@ -152,6 +152,8 @@ def test_region():
     f1 = Feature('\t'.join(gff3))
     assert f1._range == Range(999, 2000)
     assert f1.start == 999 and f1.end == 2000
+    assert f1.contains(Range(1500, 1600))
+    assert f1.contains_point(5) is False
 
     gff3 = ['contig5', 'vim', 'mRNA', '500', '2500', '.', '+', '.',
             'ID=t1;Parent=g1']

tests/test_range.py

@@ -108,6 +108,8 @@ def test_contains_within():
     assert Range(279886, 283581).contains(Range(279986, 283481)) is True
     assert Range(279986, 283481).contains(Range(279886, 283581)) is False
     assert Range(279986, 283481).within(Range(279886, 283581)) is True
+    assert Range(9876, 9999).contains_point(10) is False
+    assert Range(9876, 9999).contains_point(9900) is True
 
 
 def test_transform():