added tests for distance/search functions

Author: iskandr

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))