def setUp(self):
self.dg = DGE("data/read.bam", "data/gene.gtf", feature_type="exon",
id_feature="gene_id", id_count="gene_id")
self.dc = DGE("data/read.bam", "data/gene.gtf", feature_type="exon",
id_feature="gene_id", id_count="cluster_id")
class DGE_Test(unittest.TestCase):
def setUp(self):
self.dg = DGE("data/read.bam", "data/gene.gtf", feature_type="exon",
id_feature="gene_id", id_count="gene_id")
self.dc = DGE("data/read.bam", "data/gene.gtf", feature_type="exon",
id_feature="gene_id", id_count="cluster_id")
def test_gas(self):
assert self.dg.gas.stranded
def test_fid2cid(self):
assert self.dg.fid2cid['g2'] == 'g2'
assert self.dc.fid2cid['g2'] == '1'
def test_cid2counter(self):
assert 'g2' in self.dg.cid2counter
assert '1' in self.dc.cid2counter
def test_cid2length(self):
assert self.dg.cid2length['g2'] == 300
assert self.dc.cid2length['1'] == 400
def test_iter_reads(self):
assert len([r for r in self.dg.iter_reads()]) == 16
def test_count_unique(self):
self.dg.count_unique()
assert self.dg.nunique == 5
assert self.dg.nshared == 1
def test_count_shared(self):
self.dg.count_unique()
self.dg.count_shared()
assert self.dg.cid2counter['g2'].shared == 0.5
self.dc.count_unique()
self.dc.count_shared()
assert self.dc.cid2counter['1'].shared == 1 #
def test_read2features(self):
iv = HTSeq.GenomicInterval('chr1', 1600, 1620, '+')
assert sorted(self.dg.read2features((iv,))) == ['g1', 'g2']
assert sorted(self.dc.read2features((iv,))) == ['g1', 'g2']
