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)
