Merge pull request #39 from hammerlab/search_over_loci

Search over loci

Author: iskandr

pyensembl/__init__.py

@@ -6,4 +6,5 @@
 from .gtf import GTF
 from .locus import Locus
 from .reference_transcripts import ReferenceTranscripts
-from .transcript import Transcript
+from .search import find_nearest_locus
+from .transcript import Transcript

pyensembl/locus.py

@@ -171,6 +171,27 @@ def can_overlap(self, contig, strand=None):
             and
             (strand is None or self.on_strand(strand)))
 
+    def distance_to_interval(self, start, end):
+        """
+        Find the distance between intervals [start1, end1] and [start2, end2].
+        If the intervals overlap then the distance is 0.
+        """
+        if self.start > end:
+            # interval is before this exon
+            return self.start - end
+        elif self.end < start:
+            # exon is before the interval
+            return start - self.end
+        else:
+            return 0
+
+    def distance_to_locus(self, other):
+        if not self.can_overlap(other.contig, other.strand):
+            # if two loci are on different contigs or strands,
+            # can't compute a distance between them
+            return float("inf")
+        return self.distance_to_interval(other.start, other.end)
+
     def overlaps(self, contig, start, end, strand=None):
         """
         Does this locus overlap with a given range of positions?
@@ -181,9 +202,7 @@ def overlaps(self, contig, start, end, strand=None):
         return (
             self.can_overlap(contig, strand)
             and
-            end >= self.start
-            and
-            start <= self.end)
+            self.distance_to_interval(start, end) == 0)
 
     def overlaps_locus(self, other_locus):
         return self.overlaps(
@@ -205,4 +224,4 @@ def contains_locus(self, other_locus):
             other_locus.contig,
             other_locus.start,
             other_locus.end,
-            other_locus.strand)
+            other_locus.strand)

pyensembl/search.py

@@ -0,0 +1,20 @@
+"""
+Helper functions for searching over collections of PyEnsembl objects
+"""
+
+def find_nearest_locus(start, end, loci):
+    """
+    Finds nearest locus (object with method `distance_to_interval`) to the
+    interval defined by the given `start` and `end` positions.
+    Returns the distance to that locus, along with the locus object itself.
+    """
+    best_distance = float("inf")
+    best_locus = None
+    for locus in loci:
+        distance = locus.distance_to_interval(start, end)
+
+        if best_distance > distance:
+            best_distance = distance
+            best_locus = locus
+
+    return best_distance, best_locus

setup.py

@@ -31,7 +31,7 @@
 if __name__ == '__main__':
     setup(
         name='pyensembl',
-        version="0.5.3",
+        version="0.5.4",
         description="Python interface to ensembl reference genome metadata",
       	author="Alex Rubinsteyn",
         author_email="alex {dot} rubinsteyn {at} mssm {dot} edu",

test/test_locus.py

@@ -2,7 +2,6 @@
 
 from nose.tools import assert_raises
 
-
 def test_normalize_chromosome():
     assert normalize_chromosome("X") == "X"
     assert normalize_chromosome("chrX") == "X"
@@ -162,4 +161,14 @@ def test_range_offset():
     with assert_raises(ValueError):
         negative_locus.offset_range(9, 10)
 
+def test_locus_distance():
+    locus_chr1_10_20_pos = Locus("1", 10, 20, "+")
+    locus_chr1_21_25_pos = Locus("1", 21, 25, "+")
+    locus_chr2_21_25_pos = Locus("2", 21, 25, "+")
+    locus_chr1_21_25_neg = Locus("1", 21, 25, "-")
+    assert locus_chr1_10_20_pos.distance_to_locus(locus_chr1_21_25_pos) == 1
+    assert locus_chr1_21_25_pos.distance_to_locus(locus_chr1_10_20_pos) == 1
+    inf = float("inf")
+    assert locus_chr1_10_20_pos.distance_to_locus(locus_chr2_21_25_pos) == inf
+    assert locus_chr1_10_20_pos.distance_to_locus(locus_chr1_21_25_neg) == inf
 

test/test_search.py

@@ -0,0 +1,55 @@
+from test_common import test_ensembl_releases
+from pyensembl import EnsemblRelease, find_nearest_locus
+from nose.tools import eq_
+
+@test_ensembl_releases
+def test_find_nearest_BRAF_exon(ensembl):
+    braf = ensembl.genes_by_name("BRAF")[0]
+    braf_transcripts = braf.transcripts
+    for exon in braf_transcripts[0].exons:
+        # immediately before exon
+        result = find_nearest_locus(
+            start=exon.start-2,
+            end=exon.end-1,
+            loci=exons)
+        eq_(result, (1, exon))
+
+        # overlapping with exon
+        result = find_nearest_locus(
+            start=exon.start-2,
+            end=exon.start+1,
+            loci=exons)
+        eq_(result, (0, exon))
+
+        # immediately after exon
+        result = find_nearest_locus(
+            start=exon.end+1,
+            end=exon.end+2,
+            loci=exons)
+        eq_(result, (1, exon))
+
+@test_ensembl_releases
+def test_find_nearest_BRAF_transcript(ensembl):
+    braf = ensembl.genes_by_name("BRAF")[0]
+    braf_transcripts = braf.transcripts
+    for transcript in braf_transcripts:
+        # immediately before transcript
+        result = find_nearest_locus(
+            start=transcript.start-2,
+            end=transcript.end-1,
+            loci=braf_transcripts)
+        eq_(result, (1, transcript))
+
+        # overlapping with transcript
+        result = find_nearest_locus(
+            start=transcript.start-2,
+            end=transcript.start+1,
+            exons=braf_transcripts)
+        eq_(result, (0, transcript))
+
+        # immediately after transcript
+        result = find_nearest_locus(
+            start=transcript.end+1,
+            end=transcript.end+2,
+            exons=braf_transcripts)
+        eq_(result, (1, transcript))