def test_test_transcripts(self):
transcripts = read_first_locus("annotate_test1.gtf")
t_dict = dict((t.attrs['transcript_id'], t) for t in transcripts)
annotate_locus(transcripts, gtf_sample_attr="sample_id")
t = t_dict['AA']
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 1)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == "B")
self.assertTrue(t.attrs[GTFAttr.TEST] == "0")
t = t_dict['BB']
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 0)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == "B")
self.assertTrue(t.attrs[GTFAttr.TEST] == "1")
t = t_dict['CC']
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 1)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == "C")
self.assertTrue(t.attrs[GTFAttr.TEST] == "1")
t = t_dict['DD']
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 3)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == "C")
self.assertTrue(t.attrs[GTFAttr.TEST] == "1")
t = t_dict['EE']
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 5)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == "C")
self.assertTrue(t.attrs[GTFAttr.TEST] == "1")
t = t_dict['FF']
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 6)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == "C")
self.assertTrue(t.attrs[GTFAttr.TEST] == "1")
def test_test_transcripts(self):
transcripts = read_first_locus("annotate_test1.gtf")
t_dict = dict((t.attrs["transcript_id"], t) for t in transcripts)
annotate_locus(transcripts, gtf_sample_attr="sample_id")
t = t_dict["AA"]
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 1)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == "B")
self.assertTrue(t.attrs[GTFAttr.TEST] == "0")
t = t_dict["BB"]
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 0)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == "B")
self.assertTrue(t.attrs[GTFAttr.TEST] == "1")
t = t_dict["CC"]
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 1)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == "C")
self.assertTrue(t.attrs[GTFAttr.TEST] == "1")
t = t_dict["DD"]
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 3)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == "C")
self.assertTrue(t.attrs[GTFAttr.TEST] == "1")
t = t_dict["EE"]
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 5)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == "C")
self.assertTrue(t.attrs[GTFAttr.TEST] == "1")
t = t_dict["FF"]
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 6)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == "C")
self.assertTrue(t.attrs[GTFAttr.TEST] == "1")
def test_find_best_match(self):
transcripts = read_first_locus("annotate_best_match1.gtf")
t_dict = dict((t.attrs['transcript_id'], t) for t in transcripts)
annotate_locus(transcripts, gtf_sample_attr="sample_id")
t = t_dict['T1']
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 0)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == 'D')
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_INTRON_RATIO], 1.0, 2)
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_COV_RATIO], 0.9375, 2)
t = t_dict['T2']
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 0)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == 'B')
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_INTRON_RATIO], 0.25, 2)
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_COV_RATIO], 0.6744, 2)
def test_find_best_match(self):
transcripts = read_first_locus("annotate_best_match1.gtf")
t_dict = dict((t.attrs["transcript_id"], t) for t in transcripts)
annotate_locus(transcripts, gtf_sample_attr="sample_id")
t = t_dict["T1"]
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 0)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == "D")
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_INTRON_RATIO], 1.0, 2)
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_COV_RATIO], 0.9375, 2)
t = t_dict["T2"]
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 0)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == "B")
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_INTRON_RATIO], 0.25, 2)
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_COV_RATIO], 0.6744, 2)
def test_intergenic(self):
transcripts = read_first_locus("annotate_intergenic1.gtf")
t_dict = dict((t.attrs['transcript_id'], t) for t in transcripts)
annotate_locus(transcripts, gtf_sample_attr="sample_id")
t = t_dict['T1']
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 6)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == 'na')
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_INTRON_RATIO], 0.0, 2)
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_COV_RATIO], 0.0, 2)
self.assertAlmostEqual(t.attrs[GTFAttr.MEAN_RECURRENCE], 2.0, 2)
self.assertAlmostEqual(t.attrs[GTFAttr.MEAN_SCORE], 20.0, 2)
t = t_dict['F']
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 6)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == 'na')
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_INTRON_RATIO], 0.0, 2)
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_COV_RATIO], 0.0, 2)
self.assertAlmostEqual(t.attrs[GTFAttr.MEAN_RECURRENCE], 2.0, 2)
self.assertAlmostEqual(t.attrs[GTFAttr.MEAN_SCORE], 20.0, 2)
def test_intergenic(self):
transcripts = read_first_locus("annotate_intergenic1.gtf")
t_dict = dict((t.attrs["transcript_id"], t) for t in transcripts)
annotate_locus(transcripts, gtf_sample_attr="sample_id")
t = t_dict["T1"]
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 6)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == "na")
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_INTRON_RATIO], 0.0, 2)
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_COV_RATIO], 0.0, 2)
self.assertAlmostEqual(t.attrs[GTFAttr.MEAN_RECURRENCE], 2.0, 2)
self.assertAlmostEqual(t.attrs[GTFAttr.MEAN_SCORE], 20.0, 2)
t = t_dict["F"]
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 6)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == "na")
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_INTRON_RATIO], 0.0, 2)
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_COV_RATIO], 0.0, 2)
self.assertAlmostEqual(t.attrs[GTFAttr.MEAN_RECURRENCE], 2.0, 2)
self.assertAlmostEqual(t.attrs[GTFAttr.MEAN_SCORE], 20.0, 2)
def test_categories(self):
transcripts = read_first_locus("annotate_category1.gtf")
t_dict = dict((t.attrs['transcript_id'], t) for t in transcripts)
annotate_locus(transcripts, gtf_sample_attr="sample_id")
# intronic same strand
self.assertTrue(t_dict['T2'].attrs[GTFAttr.CATEGORY] == 2)
# intronic opposite strand
self.assertTrue(t_dict['T3'].attrs[GTFAttr.CATEGORY] == 3)
# intronic ambiguous
self.assertTrue(t_dict['T6'].attrs[GTFAttr.CATEGORY] == 4)
# interleaving
self.assertTrue(t_dict['T4'].attrs[GTFAttr.CATEGORY] == 5)
# interleaving
self.assertTrue(t_dict['T5'].attrs[GTFAttr.CATEGORY] == 3)
# opp strand overlap (no introns)
t = t_dict['T7']
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 1)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == 'T1')
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_COV_RATIO], 0.2, 2)
# same strand overlap (no introns)
t = t_dict['T8']
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 0)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == 'T1')
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_INTRON_RATIO], 0.0, 2)
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_COV_RATIO], 0.10, 2)
# same strand overlap (with introns)
t = t_dict['T9']
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 0)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == 'T1')
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_INTRON_RATIO], 0.4, 2)
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_COV_RATIO], 2. / 3, 2)
# another same strand overlap (with introns)
t = t_dict['T10']
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 0)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == 'T1')
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_INTRON_RATIO], 0.5, 2)
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_COV_RATIO], 0.6, 2)
def test_categories(self):
transcripts = read_first_locus("annotate_category1.gtf")
t_dict = dict((t.attrs["transcript_id"], t) for t in transcripts)
annotate_locus(transcripts, gtf_sample_attr="sample_id")
# intronic same strand
self.assertTrue(t_dict["T2"].attrs[GTFAttr.CATEGORY] == 2)
# intronic opposite strand
self.assertTrue(t_dict["T3"].attrs[GTFAttr.CATEGORY] == 3)
# intronic ambiguous
self.assertTrue(t_dict["T6"].attrs[GTFAttr.CATEGORY] == 4)
# interleaving
self.assertTrue(t_dict["T4"].attrs[GTFAttr.CATEGORY] == 5)
# interleaving
self.assertTrue(t_dict["T5"].attrs[GTFAttr.CATEGORY] == 3)
# opp strand overlap (no introns)
t = t_dict["T7"]
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 1)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == "T1")
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_COV_RATIO], 0.2, 2)
# same strand overlap (no introns)
t = t_dict["T8"]
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 0)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == "T1")
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_INTRON_RATIO], 0.0, 2)
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_COV_RATIO], 0.10, 2)
# same strand overlap (with introns)
t = t_dict["T9"]
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 0)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == "T1")
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_INTRON_RATIO], 0.4, 2)
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_COV_RATIO], 2.0 / 3, 2)
# another same strand overlap (with introns)
t = t_dict["T10"]
self.assertTrue(t.attrs[GTFAttr.CATEGORY] == 0)
self.assertTrue(t.attrs[GTFAttr.ANN_REF_ID] == "T1")
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_INTRON_RATIO], 0.5, 2)
self.assertAlmostEqual(t.attrs[GTFAttr.ANN_COV_RATIO], 0.6, 2)