def test_trim_intron_retention(self):
transcripts = read_first_locus("trim_intron_retention1.gtf",
score_attr="FPKM")
GG = get_transcript_graphs(transcripts)
G, tmap = GG[POS_STRAND]
# trim at different thresholds
trim_nodes = trim_graph(G,
POS_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.01)
correct = set()
self.assertTrue(trim_nodes == correct)
trim_nodes = trim_graph(G,
POS_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.11)
correct = set([Exon(500, 1500)])
self.assertTrue(trim_nodes == correct)
trim_nodes = trim_graph(G,
POS_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.21)
correct = set([Exon(500, 1500), Exon(2000, 9000)])
self.assertTrue(trim_nodes == correct)
trim_nodes = trim_graph(G,
POS_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=1.0)
correct = set([Exon(500, 1500), Exon(2000, 9000)])
self.assertTrue(trim_nodes == correct)
def test_trim_intron_retention(self):
transcripts = read_first_locus("trim_intron_retention1.gtf", score_attr="FPKM")
GG = get_transcript_graphs(transcripts)
G,tmap = GG[POS_STRAND]
# trim at different thresholds
trim_nodes = trim_graph(G, POS_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.01)
correct = set()
self.assertTrue(trim_nodes == correct)
trim_nodes = trim_graph(G, POS_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.11)
correct = set([Exon(500,1500)])
self.assertTrue(trim_nodes == correct)
trim_nodes = trim_graph(G, POS_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.21)
correct = set([Exon(500,1500), Exon(2000,9000)])
self.assertTrue(trim_nodes == correct)
trim_nodes = trim_graph(G, POS_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=1.0)
correct = set([Exon(500,1500), Exon(2000,9000)])
self.assertTrue(trim_nodes == correct)
def test_trim_bidir(self):
transcripts = read_first_locus("trim_bidir1.gtf", score_attr="FPKM")
GG = get_transcript_graphs(transcripts)
G,tmap = GG[POS_STRAND]
# trim at three different thresholds
trim_nodes = trim_graph(G, POS_STRAND,
min_trim_length=0,
trim_utr_fraction=0.015,
trim_intron_fraction=0.0)
correct = set([Exon(0,100), Exon(900,1000)])
self.assertTrue(trim_nodes == correct)
trim_nodes = trim_graph(G, POS_STRAND,
min_trim_length=0,
trim_utr_fraction=0.11,
trim_intron_fraction=0.0)
correct = set([Exon(0,100), Exon(900,1000),
Exon(100,200), Exon(800,900)])
self.assertTrue(trim_nodes == correct)
trim_nodes = trim_graph(G, POS_STRAND,
min_trim_length=0,
trim_utr_fraction=0.26,
trim_intron_fraction=0.0)
correct = set([Exon(0,100), Exon(900,1000),
Exon(100,200), Exon(800,900),
Exon(200,300), Exon(700,800)])
self.assertTrue(trim_nodes == correct)
# flip sign of transcripts and try again
for t in transcripts:
t.strand = NEG_STRAND
GG = get_transcript_graphs(transcripts)
G,tmap = GG[NEG_STRAND]
# trim at three different thresholds
trim_nodes = trim_graph(G, NEG_STRAND,
min_trim_length=0,
trim_utr_fraction=0.015,
trim_intron_fraction=0.0)
correct = set([Exon(0,100), Exon(900,1000)])
self.assertTrue(trim_nodes == correct)
trim_nodes = trim_graph(G, NEG_STRAND,
min_trim_length=0,
trim_utr_fraction=0.11,
trim_intron_fraction=0.0)
correct = set([Exon(0,100), Exon(900,1000),
Exon(100,200), Exon(800,900)])
self.assertTrue(trim_nodes == correct)
trim_nodes = trim_graph(G, NEG_STRAND,
min_trim_length=0,
trim_utr_fraction=0.26,
trim_intron_fraction=0.0)
correct = set([Exon(0,100), Exon(900,1000),
Exon(100,200), Exon(800,900),
Exon(200,300), Exon(700,800)])
self.assertTrue(trim_nodes == correct)
def test_trim_intron_bidir(self):
transcripts = read_first_locus("trim_intron_bidir1.gtf",
score_attr="FPKM")
GG = get_transcript_graphs(transcripts)
G, tmap = GG[POS_STRAND]
# trim at different thresholds
trim_nodes = trim_graph(G,
POS_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.001)
correct = set()
self.assertTrue(trim_nodes == correct)
trim_nodes = trim_graph(G,
POS_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.025)
correct = set([Exon(1900, 2000), Exon(1000, 1100)])
self.assertTrue(trim_nodes == correct)
trim_nodes = trim_graph(G,
POS_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.2)
correct = set([
Exon(1900, 2000),
Exon(1100, 1200),
Exon(1800, 1900),
Exon(1000, 1100)
])
self.assertTrue(trim_nodes == correct)
trim_nodes = trim_graph(G,
POS_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.25)
correct = set([
Exon(1900, 2000),
Exon(1100, 1200),
Exon(1200, 1300),
Exon(1700, 1800),
Exon(1800, 1900),
Exon(1000, 1100)
])
self.assertTrue(trim_nodes == correct)
# flip sign of transcripts and try again
for t in transcripts:
t.strand = NEG_STRAND
GG = get_transcript_graphs(transcripts)
G, tmap = GG[NEG_STRAND]
# trim at different thresholds
trim_nodes = trim_graph(G,
NEG_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.001)
correct = set()
self.assertTrue(trim_nodes == correct)
trim_nodes = trim_graph(G,
NEG_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.025)
correct = set([Exon(1900, 2000), Exon(1000, 1100)])
self.assertTrue(trim_nodes == correct)
trim_nodes = trim_graph(G,
NEG_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.2)
correct = set([
Exon(1900, 2000),
Exon(1100, 1200),
Exon(1800, 1900),
Exon(1000, 1100)
])
self.assertTrue(trim_nodes == correct)
trim_nodes = trim_graph(G,
NEG_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.25)
correct = set([
Exon(1900, 2000),
Exon(1100, 1200),
Exon(1200, 1300),
Exon(1700, 1800),
Exon(1800, 1900),
Exon(1000, 1100)
])
self.assertTrue(trim_nodes == correct)
def test_trim_intronic_utr(self):
transcripts = read_first_locus("trim_intron_utr1.gtf", score_attr="FPKM")
GG = get_transcript_graphs(transcripts)
G,tmap = GG[POS_STRAND]
# trim at different thresholds
trim_nodes = trim_graph(G, POS_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.001)
correct = set()
self.assertTrue(trim_nodes == correct)
trim_nodes = trim_graph(G, POS_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.011)
correct = set([Exon(1000,1100)])
self.assertTrue(trim_nodes == correct)
trim_nodes = trim_graph(G, POS_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.055)
correct = set([Exon(1000,1100), Exon(1100,1200)])
self.assertTrue(trim_nodes == correct)
trim_nodes = trim_graph(G, POS_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.15)
correct = set([Exon(1000,1100), Exon(1100,1200),
Exon(1200,1300)])
self.assertTrue(trim_nodes == correct)
trim_nodes = trim_graph(G, POS_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=1.0)
correct = set([Exon(1000,1100), Exon(1100,1200),
Exon(1200,1300), Exon(1300,1500)])
self.assertTrue(trim_nodes == correct)
# flip sign of transcripts and try again
for t in transcripts:
t.strand = NEG_STRAND
GG = get_transcript_graphs(transcripts)
G,tmap = GG[NEG_STRAND]
# trim at different thresholds
trim_nodes = trim_graph(G, NEG_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.001)
correct = set()
self.assertTrue(trim_nodes == correct)
trim_nodes = trim_graph(G, NEG_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.011)
correct = set([Exon(1000,1100)])
self.assertTrue(trim_nodes == correct)
trim_nodes = trim_graph(G, NEG_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.055)
correct = set([Exon(1000,1100), Exon(1100,1200)])
self.assertTrue(trim_nodes == correct)
trim_nodes = trim_graph(G, NEG_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=0.15)
correct = set([Exon(1000,1100), Exon(1100,1200),
Exon(1200,1300)])
self.assertTrue(trim_nodes == correct)
trim_nodes = trim_graph(G, NEG_STRAND,
min_trim_length=0,
trim_utr_fraction=0.0,
trim_intron_fraction=1.0)
correct = set([Exon(1000,1100), Exon(1100,1200),
Exon(1200,1300), Exon(1300,1500)])
self.assertTrue(trim_nodes == correct)
