Added protein coding biotype tests (#166)

* added unit tests for Transcript.biotype and Gene.biotype

* version bump

Author: iskandr

pyensembl/__init__.py

@@ -35,7 +35,7 @@
 )
 from .transcript import Transcript
 
-__version__ = '1.0.0'
+__version__ = '1.0.1'
 
 def cached_release(release, species="human"):
     """

test/test_gene_objects.py

@@ -1,23 +1,25 @@
 from __future__ import absolute_import
 
+from nose.tools import eq_
+
 from .common import test_ensembl_releases
 from .data import TP53_gene_id
 
 @test_ensembl_releases()
-def test_TP53_gene_object_by_id(ensembl):
+def test_TP53_gene_object_by_id(genome):
     # when we look up TP53 by its gene ID, we should get the
     # correct gene back
-    gene = ensembl.gene_by_id(TP53_gene_id)
+    gene = genome.gene_by_id(TP53_gene_id)
     assert gene.name == "TP53", \
         "Incorrect gene name %s for gene ID %s in %s" % (
-            gene.name, gene.id, ensembl)
+            gene.name, gene.id, genome)
     assert gene.contig == "17", \
         "Incorrect gene contig %s for gene ID %s in %s" % (
-            gene.contig, gene.id, ensembl)
+            gene.contig, gene.id, genome)
 
 @test_ensembl_releases()
-def test_TP53_gene_object_by_name(ensembl):
-    genes = ensembl.genes_by_name("TP53")
+def test_TP53_gene_object_by_name(genome):
+    genes = genome.genes_by_name("TP53")
     # we should only have one TP53 gene (there aren't any copies)
     assert len(genes) == 1, \
         "Expected only one gene with name TP53, got %s" % (genes,)
@@ -26,17 +28,23 @@ def test_TP53_gene_object_by_name(ensembl):
         "Expected gene to have ID %s, got %s" % (TP53_gene_id, genes[0].id)
 
 @test_ensembl_releases()
-def test_equal_genes(ensembl):
-    gene1 = ensembl.genes_by_name("TP53")[0]
+def test_equal_genes(genome):
+    gene1 = genome.genes_by_name("TP53")[0]
     # get an identical gene
-    gene2 = ensembl.gene_by_id(gene1.id)
+    gene2 = genome.gene_by_id(gene1.id)
 
     assert hash(gene1) == hash(gene2)
     assert gene1 == gene2
 
 @test_ensembl_releases()
-def test_not_equal_genes(release):
-    gene1 = release.genes_by_name("MUC1")[0]
-    gene2 = release.genes_by_name("BRCA1")[0]
+def test_not_equal_genes(genome):
+    gene1 = genome.genes_by_name("MUC1")[0]
+    gene2 = genome.genes_by_name("BRCA1")[0]
     assert hash(gene1) != hash(gene2)
     assert gene1 != gene2
+
+@test_ensembl_releases()
+def test_BRCA1_protein_coding_biotype(genome):
+    gene = genome.genes_by_name("BRCA1")[0]
+    assert gene.is_protein_coding
+    eq_(gene.biotype, "protein_coding")

test/test_transcript_objects.py

@@ -77,10 +77,10 @@ def test_transcript_exons():
 # TODO: Add gene_id patching to gtf_parsing, add ensembl54 to the list
 # below
 @test_ensembl_releases(75, 77)
-def test_sequence_parts(ensembl):
+def test_sequence_parts(genome):
     # Ensure that the UTRs and coding sequence can be
     # combined to make the full transcript.
-    transcript = ensembl.transcript_by_id(FOXP3_001_transcript_id)
+    transcript = genome.transcript_by_id(FOXP3_001_transcript_id)
 
     # The combined lengths of the upstream untranslated region,
     # coding sequence, and downstream untranslated region
@@ -149,17 +149,17 @@ def test_transcript_cds_CTNNIP1_004():
     eq_(cds, CTNNBIP1_004_CDS)
 
 @test_ensembl_releases()
-def test_equal_transcripts(ensembl):
-    t1 = ensembl.transcripts_by_name("TP53-001")[0]
+def test_equal_transcripts(genome):
+    t1 = genome.transcripts_by_name("TP53-001")[0]
     # get an identical gene
-    t2 = ensembl.transcript_by_id(t1.id)
+    t2 = genome.transcript_by_id(t1.id)
     eq_(t1, t2)
     eq_(hash(t1), hash(t2))
 
 @test_ensembl_releases()
-def test_not_equal_transcripts(release):
-    t1 = release.transcripts_by_name("MUC1-001")[0]
-    t2 = release.transcripts_by_name("BRCA1-001")[0]
+def test_not_equal_transcripts(genome):
+    t1 = genome.transcripts_by_name("MUC1-001")[0]
+    t2 = genome.transcripts_by_name("BRCA1-001")[0]
     assert_not_equal(t1, t2)
 
 def test_protein_id():
@@ -174,3 +174,9 @@ def test_transcript_gene_should_match_parent_gene():
     gene = ensembl77.gene_by_id(TP53_gene_id)
     for transcript in gene.transcripts:
         eq_(transcript.gene, gene)
+
+@test_ensembl_releases()
+def test_BRCA1_001_has_protein_coding_biotype(genome):
+    transcript = genome.transcripts_by_name("BRCA1-001")[0]
+    assert transcript.is_protein_coding
+    eq_(transcript.biotype, "protein_coding")