def test_resolve_strand_scores1(self): transcripts = read_first_locus("resolve_strand_scores1.gtf", score_attr="FPKM") tdict = dict((t.attrs['transcript_id'],t) for t in transcripts) partition_transcripts_by_strand(transcripts) # check strands t = tdict["AA"] self.assertTrue(t.strand == NO_STRAND) t = tdict["BB"] self.assertTrue(t.strand == NO_STRAND)
def test_resolve_strand_scores1(self): transcripts = read_first_locus("resolve_strand_scores1.gtf", score_attr="FPKM") tdict = dict((t.attrs['transcript_id'], t) for t in transcripts) partition_transcripts_by_strand(transcripts) # check strands t = tdict["AA"] self.assertTrue(t.strand == NO_STRAND) t = tdict["BB"] self.assertTrue(t.strand == NO_STRAND)
def test_resolve_strand_scores3(self): transcripts = read_first_locus("resolve_strand_scores3.gtf", score_attr="FPKM") tdict = dict((t.attrs['transcript_id'],t) for t in transcripts) partition_transcripts_by_strand(transcripts) # check strands t = tdict['CC'] self.assertTrue(t.strand == POS_STRAND) t = tdict['DD'] self.assertTrue(t.strand == NEG_STRAND) t = tdict['EE'] self.assertTrue(t.strand == POS_STRAND) # increase score on negative strand transcripts = read_first_locus("resolve_strand_scores3.gtf", score_attr="FPKM") tdict = dict((t.attrs['transcript_id'],t) for t in transcripts) tdict['DD'].score += 1.0 partition_transcripts_by_strand(transcripts) # check strands t = tdict['EE'] self.assertTrue(t.strand == NEG_STRAND)
def test_resolve_strand_ref(self): transcripts = read_first_locus("resolve_strand_ref1.gtf", score_attr="FPKM") tdict = dict((t.attrs['transcript_id'],t) for t in transcripts) partition_transcripts_by_strand(transcripts) # check resolved strands t = tdict["T1"] self.assertTrue(t.strand == POS_STRAND) t = tdict["T2"] self.assertTrue(t.strand == NEG_STRAND) # equal overlap on both strands, default to positive t = tdict["T3"] self.assertTrue(t.strand == POS_STRAND) # more positive strand overlap t = tdict["T4"] self.assertTrue(t.strand == POS_STRAND) # more negative strand overlap t = tdict["T5"] self.assertTrue(t.strand == NEG_STRAND) return
def test_resolve_strand_ref(self): transcripts = read_first_locus("resolve_strand_ref1.gtf", score_attr="FPKM") tdict = dict((t.attrs['transcript_id'], t) for t in transcripts) partition_transcripts_by_strand(transcripts) # check resolved strands t = tdict["T1"] self.assertTrue(t.strand == POS_STRAND) t = tdict["T2"] self.assertTrue(t.strand == NEG_STRAND) # equal overlap on both strands, default to positive t = tdict["T3"] self.assertTrue(t.strand == POS_STRAND) # more positive strand overlap t = tdict["T4"] self.assertTrue(t.strand == POS_STRAND) # more negative strand overlap t = tdict["T5"] self.assertTrue(t.strand == NEG_STRAND) return
def test_resolve_strand_scores3(self): transcripts = read_first_locus("resolve_strand_scores3.gtf", score_attr="FPKM") tdict = dict((t.attrs['transcript_id'], t) for t in transcripts) partition_transcripts_by_strand(transcripts) # check strands t = tdict['CC'] self.assertTrue(t.strand == POS_STRAND) t = tdict['DD'] self.assertTrue(t.strand == NEG_STRAND) t = tdict['EE'] self.assertTrue(t.strand == POS_STRAND) # increase score on negative strand transcripts = read_first_locus("resolve_strand_scores3.gtf", score_attr="FPKM") tdict = dict((t.attrs['transcript_id'], t) for t in transcripts) tdict['DD'].score += 1.0 partition_transcripts_by_strand(transcripts) # check strands t = tdict['EE'] self.assertTrue(t.strand == NEG_STRAND)