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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(genome):
# when we look up TP53 by its gene ID, we should get the
# correct gene back
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, genome)
assert gene.contig == "17", \
"Incorrect gene contig %s for gene ID %s in %s" % (
gene.contig, gene.id, genome)
@test_ensembl_releases()
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,)
# make sure it has the correct gene ID
assert genes[0].id == TP53_gene_id, \
"Expected gene to have ID %s, got %s" % (TP53_gene_id, genes[0].id)
@test_ensembl_releases()
def test_equal_genes(genome):
gene1 = genome.genes_by_name("TP53")[0]
# get an identical gene
gene2 = genome.gene_by_id(gene1.id)
assert hash(gene1) == hash(gene2)
assert gene1 == gene2
@test_ensembl_releases()
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")
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