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)