def test_retrieve_supplementary_alignment_from_primary(self):
alignment_it = self.alignment_file.fetch(until_eof=True)
alignments = list(alignment_it)
for i in range(10, 30, 2):
primary = alignments[i]
supplementary = alignments[i + 1]
retrieved_supplementary_alns = retrieve_other_alignments(
primary, self.alignment_file)
self.assertEqual(len(retrieved_supplementary_alns), 1)
self.assertEqual(retrieved_supplementary_alns[0].cigarstring,
supplementary.cigarstring.replace("H", "S"))
self.assertEqual(retrieved_supplementary_alns[0].reference_id,
supplementary.reference_id)
self.assertEqual(retrieved_supplementary_alns[0].reference_start,
supplementary.reference_start)
self.assertEqual(retrieved_supplementary_alns[0].reference_end,
supplementary.reference_end)
self.assertEqual(retrieved_supplementary_alns[0].flag,
supplementary.flag)
self.assertEqual(retrieved_supplementary_alns[0].mapping_quality,
supplementary.mapping_quality)
self.assertEqual(
retrieved_supplementary_alns[0].query_sequence[
retrieved_supplementary_alns[0].query_alignment_start:
retrieved_supplementary_alns[0].query_alignment_end],
supplementary.query_sequence)
self.assertEqual(retrieved_supplementary_alns[0].query_name,
supplementary.query_name)
def test_retrieve_primary_alignment_from_supplementary(self):
alignment_it = self.alignment_file.fetch(until_eof=True)
alignments = list(alignment_it)
for i in range(10, 30, 2):
primary = alignments[i]
supplementary = alignments[i + 1]
retrieved_primary_alns = retrieve_other_alignments(
supplementary, self.alignment_file)
self.assertEqual(len(retrieved_primary_alns), 0)
def test_satag_extraction_complete(self):
primary = self.alignments[0]
supplementary_alns = retrieve_other_alignments(primary, self.samfile)
for index, aln in enumerate(supplementary_alns):
self.assertEqual(aln.cigarstring,
self.alignments[index + 1].cigarstring)
self.assertEqual(aln.reference_id,
self.alignments[index + 1].reference_id)
self.assertEqual(aln.reference_start,
self.alignments[index + 1].reference_start)
self.assertEqual(aln.reference_end,
self.alignments[index + 1].reference_end)
self.assertEqual(aln.flag, self.alignments[index + 1].flag)
self.assertEqual(aln.mapping_quality,
self.alignments[index + 1].mapping_quality)
self.assertEqual(aln.query_sequence,
self.alignments[index + 1].query_sequence)
self.assertEqual(aln.query_name,
self.alignments[index + 1].query_name)
self.assertEqual(aln.query_alignment_start,
self.alignments[index + 1].query_alignment_start)
self.assertEqual(aln.query_alignment_end,
self.alignments[index + 1].query_alignment_end)
def test_satag_negative_mapq(self):
primary = self.alignments[1]
supplementary_alns = retrieve_other_alignments(primary, self.samfile)
#negative mapping quality is interpreted as 0
self.assertEqual(len(supplementary_alns), 1)
self.assertEqual(supplementary_alns[0].mapping_quality, 0)
def test_satag_too_many_fields(self):
primary = self.alignments[0]
supplementary_alns = retrieve_other_alignments(primary, self.samfile)
#first SA entry has too many fields
self.assertEqual(len(supplementary_alns), 2)
def test_satag_length(self):
primary = self.alignments[0]
supplementary_alns = retrieve_other_alignments(primary, self.samfile)
self.assertEqual(len(supplementary_alns), 3)