def testDebugReportsOnReverseRead(self):
samIO = StringIO.StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M3I2M\t=\t1\t8\tACTGGGAG\tJJJJJJJJ\n"
"test1\t147\ttest\t5\t44\t8M\t=\t1\t-8\tGACCCAAC\tJJJJJIJJ\n"
"test1\t99\ttest\t1\t44\t3M3I2M\t=\t1\t12\tATTGGGAG\tJJJJJJJJ\n"
"test1\t147\ttest\t5\t44\t8M\t=\t1\t-12\tGACCCAAC\tJJJJJHJJ\n")
reports = {('test', 10): None}
expected_reports = {('test', 10): 'H{A: 2}, I{A: 1}'}
remap.sam_to_conseqs(samIO, debug_reports=reports)
self.assertDictEqual(expected_reports, reports)
def testDebugReports(self):
samIO = StringIO.StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M3I9M\t=\t1\t12\tACTGGGAGACCCAAC\tJIJJJJJJJJJJJJJ\n"
"test1\t147\ttest\t1\t44\t3M3I9M\t=\t1\t-12\tACTGGGAGACCCAAC\tJIJJJJJJJJJJJJJ\n"
"test1\t99\ttest\t1\t44\t3M3I9M\t=\t1\t12\tATTGGGAGACCCAAC\tJHJJJJJJJJJJJJJ\n"
"test1\t147\ttest\t1\t44\t3M3I9M\t=\t1\t-12\tATTGGGAGACCCAAC\tJHJJJJJJJJJJJJJ\n"
)
reports = {('test', 2): None}
expected_reports = {('test', 2): 'H{C: 1, T: 1}, I{C: 1}'}
remap.sam_to_conseqs(samIO, debug_reports=reports)
self.assertDictEqual(expected_reports, reports)
def testDebugReports(self):
sam_file = StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M3I9M\t=\t1\t12\tACTGGGAGACCCAAC\tJIJJJJJJJJJJJJJ\n"
"test1\t147\ttest\t1\t44\t3M3I9M\t=\t1\t-12\tACTGGGAGACCCAAC\tJIJJJJJJJJJJJJJ\n"
"test1\t99\ttest\t1\t44\t3M3I9M\t=\t1\t12\tATTGGGAGACCCAAC\tJHJJJJJJJJJJJJJ\n"
"test1\t147\ttest\t1\t44\t3M3I9M\t=\t1\t-12\tATTGGGAGACCCAAC\tJHJJJJJJJJJJJJJ\n"
)
reports = {('test', 2): None}
expected_reports = {('test', 2): 'H{C: 1, T: 1}, I{C: 1}'}
remap.sam_to_conseqs(sam_file, debug_reports=reports)
self.assertDictEqual(expected_reports, reports)
def testDebugReportsOnReverseRead(self):
sam_file = StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M3I2M\t=\t1\t8\tACTGGGAG\tJJJJJJJJ\n"
"test1\t147\ttest\t5\t44\t8M\t=\t1\t-8\tGACCCAAC\tJJJJJIJJ\n"
"test1\t99\ttest\t1\t44\t3M3I2M\t=\t1\t12\tATTGGGAG\tJJJJJJJJ\n"
"test1\t147\ttest\t5\t44\t8M\t=\t1\t-12\tGACCCAAC\tJJJJJHJJ\n"
)
reports = {('test', 10): None}
expected_reports = {('test', 10): 'H{A: 2}, I{A: 1}'}
remap.sam_to_conseqs(sam_file, debug_reports=reports)
self.assertDictEqual(expected_reports, reports)
def testReverseLeftOfForward(self):
sam_file = StringIO("@SQ\tSN:test\n"
"test1\t99\ttest\t2\t44\t1M\t=\t1\t1\tC\tJ\n"
"test1\t147\ttest\t1\t44\t1M\t=\t2\t-1\tA\tJ\n")
expected_conseqs = {'test': 'AC'}
conseqs = remap.sam_to_conseqs(sam_file)
self.assertDictEqual(expected_conseqs, conseqs)
def testDeletion(self):
sam_file = StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M3D3M\t=\t3\t6\tACAGGG\tJJJJJJ\n")
expected_conseqs = {'test': 'ACAGGG'}
conseqs = remap.sam_to_conseqs(sam_file)
self.assertDictEqual(expected_conseqs, conseqs)
def testHeaderFields(self):
samIO = StringIO.StringIO(
"@SQ\tOF:other field: ignored\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M\t=\t1\t3\tACA\tJJJ\n")
expected_conseqs = {'test': 'ACA'}
conseqs = remap.sam_to_conseqs(samIO)
self.assertDictEqual(expected_conseqs, conseqs)
def testSeedsBothConverged(self):
""" Both references are now closer to the other seed than the start.
Don't drop both. Keep test because it has more reads.
"""
# SAM:qname, flag, rname, pos, mapq, cigar, rnext, pnext, tlen, seq, qual
sam_file = StringIO(
"@SQ\tSN:test\tSN:other\tSN:unrelated\n"
"test1\t99\ttest\t1\t44\t8M\t=\t1\t10\tAAGCCGTA\tJJJJJJJJJJ\n"
"test2\t99\ttest\t1\t44\t8M\t=\t1\t10\tAAGCCGTA\tJJJJJJJJJJ\n"
"other1\t99\tother\t1\t44\t8M\t=\t1\t10\tATGAAGTA\tJJJJJJJJJJ\n"
"unrelated1\t99\tunrelated\t1\t44\t9M\t=\t1\t10\tGGGTTTGGG\tJJJJJJJJJ\n"
)
seeds = {
'test': 'ATGAAGTA',
'other': 'AAGCCGAA',
'unrelated': 'GGGTTTGGG'
}
expected_conseqs = {'test': 'AAGCCGTA', 'unrelated': 'GGGTTTGGG'}
expected_distances = {
'test': dict(seed_dist=3, other_dist=1, other_seed='other'),
'other': dict(seed_dist=5, other_dist=0, other_seed='test'),
'unrelated': dict(seed_dist=0, other_dist=7, other_seed='test')
}
distances = {}
conseqs = remap.sam_to_conseqs(sam_file,
seeds=seeds,
original_seeds=seeds,
is_filtered=True,
distance_report=distances)
self.maxDiff = 1000
self.assertEqual(expected_distances, distances)
self.assertEqual(expected_conseqs, conseqs)
def testDeletionWithFrameShift(self):
samIO = StringIO.StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M1D3M\t=\t3\t6\tACAGGG\tJJJJJJ\n")
expected_conseqs = {'test': 'ACA-GGG'}
conseqs = remap.sam_to_conseqs(samIO)
self.assertDictEqual(expected_conseqs, conseqs)
def testSoftClip(self):
samIO = StringIO.StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3S5M1S\t=\t1\t9\tACAGGGAGA\tJJJJJJJJJ\n")
expected_conseqs = {'test': 'GGGAG'}
conseqs = remap.sam_to_conseqs(samIO)
self.assertDictEqual(expected_conseqs, conseqs)
def testSimpleInsertion(self):
samIO = StringIO.StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M3I3M\t=\t1\t9\tACAGGGAGA\tJJJJJJJJJ\n")
expected_conseqs = {'test': 'ACAGGGAGA'}
conseqs = remap.sam_to_conseqs(samIO)
self.assertDictEqual(expected_conseqs, conseqs)
def testSeedsConverged(self):
# SAM:qname, flag, rname, pos, mapq, cigar, rnext, pnext, tlen, seq, qual
samIO = StringIO.StringIO(
"@SQ\tSN:test\tSN:other\tSN:wayoff\n"
"test1\t99\ttest\t1\t44\t10M\t=\t1\t10\tATGAGGAGTA\tJJJJJJJJJJJJ\n"
"other1\t99\tother\t1\t44\t10M\t=\t1\t10\tATGACCAGTA\tJJJJJJJJJJJJ\n"
"wayoff1\t99\twayoff\t1\t44\t10M\t=\t1\t10\tATGAGGGTAC\tJJJJJJJJJJJJ\n"
)
seeds = {'test': 'ATGAAGTA', 'other': 'AAGCCGAA', 'wayoff': 'TCATGTAC'}
expected_conseqs = {'test': 'ATGAGGAGTA'}
expected_distances = {
'test': dict(seed_dist=2, other_dist=5, other_seed='other'),
'other': dict(seed_dist=4, other_dist=2, other_seed='test'),
'wayoff': dict(seed_dist=4, other_dist=3, other_seed='test')
}
distances = {}
conseqs = remap.sam_to_conseqs(samIO,
seeds=seeds,
is_filtered=True,
distance_report=distances)
self.maxDiff = 1000
self.assertEqual(expected_conseqs, conseqs)
self.assertEqual(expected_distances, distances)
def testLowQualityAtEnd(self):
samIO = StringIO.StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M\t=\t1\t3\tACG\tJJ/\n")
expected_conseqs = {'test': 'ACN'}
conseqs = remap.sam_to_conseqs(samIO, quality_cutoff=32)
self.assertDictEqual(expected_conseqs, conseqs)
def testUnknownReferenceName(self):
samIO = StringIO.StringIO(
"@SQ\tSN:testX\n"
"test1\t99\ttestY\t1\t44\t12M\t=\t1\t3\tACA\tJJJ\n")
expected_conseqs = {}
conseqs = remap.sam_to_conseqs(samIO)
self.assertDictEqual(expected_conseqs, conseqs)
def testSeedsConverged(self):
# SAM:qname, flag, rname, pos, mapq, cigar, rnext, pnext, tlen, seq, qual
sam_file = StringIO(
"@SQ\tSN:test\tSN:other\tSN:wayoff\n"
"test1\t99\ttest\t1\t44\t10M\t=\t1\t10\tATGAGGAGTA\tJJJJJJJJJJJJ\n"
"other1\t99\tother\t1\t44\t10M\t=\t1\t10\tATGACCAGTA\tJJJJJJJJJJJJ\n"
"wayoff1\t99\twayoff\t1\t44\t10M\t=\t1\t10\tATGAGGGTAC\tJJJJJJJJJJJJ\n"
)
seeds = {'test': 'ATGAAGTA',
'other': 'AAGCCGAA',
'wayoff': 'TCATGTAC'}
expected_conseqs = {'test': 'ATGAGGAGTA'}
expected_distances = {'test': dict(seed_dist=2,
other_dist=5,
other_seed='other'),
'other': dict(seed_dist=4,
other_dist=2,
other_seed='test'),
'wayoff': dict(seed_dist=4,
other_dist=3,
other_seed='test')}
distances = {}
conseqs = remap.sam_to_conseqs(sam_file,
seeds=seeds,
original_seeds=seeds,
is_filtered=True,
distance_report=distances)
self.maxDiff = 1000
self.assertEqual(expected_conseqs, conseqs)
self.assertEqual(expected_distances, distances)
def testInsertionAfterLowQuality(self):
samIO = StringIO.StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M3I3M\t=\t1\t9\tACAGGGAGA\tJJ/JJJJJJ\n")
expected_conseqs = {'test': 'ACNAGA'}
conseqs = remap.sam_to_conseqs(samIO, quality_cutoff=32)
self.assertDictEqual(expected_conseqs, conseqs)
def testMaxConsensus(self):
sam_file = StringIO("@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M\t=\t1\t3\tACA\tJJJ\n"
"test2\t147\ttest\t1\t44\t3M\t=\t1\t-3\tACA\tJJJ\n"
"test3\t99\ttest\t1\t44\t3M\t=\t1\t3\tTCA\tJJJ\n")
expected_conseqs = {'test': 'ACA'}
conseqs = remap.sam_to_conseqs(sam_file)
self.assertDictEqual(expected_conseqs, conseqs)
def testLowQualityAtEnd(self):
sam_file = StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M\t=\t1\t3\tACG\tJJ/\n"
)
expected_conseqs = {'test': 'ACN'}
conseqs = remap.sam_to_conseqs(sam_file, quality_cutoff=32)
self.assertDictEqual(expected_conseqs, conseqs)
def testOffset(self):
samIO = StringIO.StringIO(
"@SQ\tSN:test\n"
"test1\t147\ttest\t4\t44\t12M\t=\t3\t-12\tACAAGACCCAAC\tJJJJJJJJJJJJ\n"
)
expected_conseqs = {'test': 'NNNACAAGACCCAAC'}
conseqs = remap.sam_to_conseqs(samIO)
self.assertDictEqual(expected_conseqs, conseqs)
def testBigDeletionWithFrameShift(self):
sam_file = StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M4D3M\t=\t3\t6\tACAGGG\tJJJJJJ\n"
)
expected_conseqs = {'test': 'ACA----GGG'}
conseqs = remap.sam_to_conseqs(sam_file)
self.assertDictEqual(expected_conseqs, conseqs)
def testLowQualityForward(self):
samIO = StringIO.StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M\t=\t3\t3\tATA\tJJA\n"
"test1\t147\ttest\t3\t44\t3M\t=\t1\t-3\tGCC\tJJJ\n")
expected_conseqs = {'test': 'ATGCC'}
conseqs = remap.sam_to_conseqs(samIO)
self.assertDictEqual(expected_conseqs, conseqs)
def testInsertionAfterLowQuality(self):
sam_file = StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M3I3M\t=\t1\t9\tACAGGGAGA\tJJ/JJJJJJ\n"
)
expected_conseqs = {'test': 'ACNAGA'}
conseqs = remap.sam_to_conseqs(sam_file, quality_cutoff=32)
self.assertDictEqual(expected_conseqs, conseqs)
def testSimpleInsertion(self):
sam_file = StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M3I3M\t=\t1\t9\tACAGGGAGA\tJJJJJJJJJ\n"
)
expected_conseqs = {'test': 'ACAGGGAGA'}
conseqs = remap.sam_to_conseqs(sam_file)
self.assertDictEqual(expected_conseqs, conseqs)
def testSoftClip(self):
sam_file = StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3S5M1S\t=\t1\t9\tACAGGGAGA\tJJJJJJJJJ\n"
)
expected_conseqs = {'test': 'GGGAG'}
conseqs = remap.sam_to_conseqs(sam_file)
self.assertDictEqual(expected_conseqs, conseqs)
def testExtraFields(self):
sam_file = StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M\t=\t1\t3\tACA\tJJJ\tAS:i:236\tNM:i:12\n"
)
expected_conseqs = {'test': 'ACA'}
conseqs = remap.sam_to_conseqs(sam_file)
self.assertDictEqual(expected_conseqs, conseqs)
def testOffset(self):
sam_file = StringIO(
"@SQ\tSN:test\n"
"test1\t147\ttest\t4\t44\t12M\t=\t3\t-12\tACAAGACCCAAC\tJJJJJJJJJJJJ\n"
)
expected_conseqs = {'test': 'NNNACAAGACCCAAC'}
conseqs = remap.sam_to_conseqs(sam_file)
self.assertDictEqual(expected_conseqs, conseqs)
def testExtraFields(self):
samIO = StringIO.StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M\t=\t1\t3\tACA\tJJJ\tAS:i:236\tNM:i:12\n"
)
expected_conseqs = {'test': 'ACA'}
conseqs = remap.sam_to_conseqs(samIO)
self.assertDictEqual(expected_conseqs, conseqs)
def testTie(self):
samIO = StringIO.StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M\t=\t1\t3\tGCA\tJJJ\n"
"test2\t147\ttest\t1\t44\t3M\t=\t1\t-3\tTCA\tJJJ\n")
expected_conseqs = {'test': 'GCA'}
conseqs = remap.sam_to_conseqs(samIO)
self.assertDictEqual(expected_conseqs, conseqs)
def testUnknownReferenceName(self):
sam_file = StringIO(
"@SQ\tSN:testX\n"
"test1\t99\ttestY\t1\t44\t12M\t=\t1\t3\tACA\tJJJ\n"
)
expected_conseqs = {}
conseqs = remap.sam_to_conseqs(sam_file)
self.assertDictEqual(expected_conseqs, conseqs)
def testHeaderFields(self):
sam_file = StringIO(
"@SQ\tOF:other field: ignored\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M\t=\t1\t3\tACA\tJJJ\n"
)
expected_conseqs = {'test': 'ACA'}
conseqs = remap.sam_to_conseqs(sam_file)
self.assertDictEqual(expected_conseqs, conseqs)
def testDeletion(self):
samIO = StringIO.StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M3D3M\t=\t3\t6\tACAGGG\tJJJJJJ\n"
)
expected_conseqs = {'test': 'ACAGGG'}
conseqs = remap.sam_to_conseqs(samIO)
self.assertDictEqual(expected_conseqs, conseqs)
def testLowQuality(self):
# Note that we ignore the overlapped portion of the reverse read,
# even if it has higher quality.
sam_file = StringIO("@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M\t=\t1\t3\tACG\tJ/J\n")
expected_conseqs = {'test': 'ANG'}
conseqs = remap.sam_to_conseqs(sam_file, quality_cutoff=32)
self.assertDictEqual(expected_conseqs, conseqs)
def testInsertionAndOffset(self):
samIO = StringIO.StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M3I3M\t=\t1\t9\tACAGGGAGA\tJJJJJJJJJJJJ\n"
"test2\t99\ttest\t5\t44\t5M\t=\t1\t5\tGACCC\tJJJJJ\n")
expected_conseqs = {'test': 'ACAGGGAGACCC'}
conseqs = remap.sam_to_conseqs(samIO)
self.assertDictEqual(expected_conseqs, conseqs)
def testLowQualityForward(self):
sam_file = StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M\t=\t3\t3\tATA\tJJA\n"
"test1\t147\ttest\t3\t44\t3M\t=\t1\t-3\tGCC\tJJJ\n"
)
expected_conseqs = {'test': 'ATGCC'}
conseqs = remap.sam_to_conseqs(sam_file)
self.assertDictEqual(expected_conseqs, conseqs)
def testTie(self):
sam_file = StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M\t=\t1\t3\tGCA\tJJJ\n"
"test2\t147\ttest\t1\t44\t3M\t=\t1\t-3\tTCA\tJJJ\n"
)
expected_conseqs = {'test': 'GCA'}
conseqs = remap.sam_to_conseqs(sam_file)
self.assertDictEqual(expected_conseqs, conseqs)
def testSeedsNeedSomeReads(self):
sam_file = StringIO("@SQ\tSN:test\n"
"test1\t99\ttest\t4\t44\t3M\t=\t10\t3\tTAT\tJJJ\n")
seeds = {'test': 'ACATTTGGGCAC', 'other': 'TATGCACCC'}
expected_conseqs = {'test': 'ACATATGGGCAC'}
conseqs = remap.sam_to_conseqs(sam_file, seeds=seeds)
self.assertDictEqual(expected_conseqs, conseqs)
def testSimple(self):
# SAM:qname, flag, rname, pos, mapq, cigar, rnext, pnext, tlen, seq, qual
sam_file = StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t12M\t=\t1\t12\tACAAGACCCAAC\tJJJJJJJJJJJJ\n"
)
expected_conseqs = {'test': 'ACAAGACCCAAC'}
conseqs = remap.sam_to_conseqs(sam_file)
self.assertDictEqual(expected_conseqs, conseqs)
def testInsertionAndOffset(self):
sam_file = StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M3I3M\t=\t1\t9\tACAGGGAGA\tJJJJJJJJJJJJ\n"
"test2\t99\ttest\t5\t44\t5M\t=\t1\t5\tGACCC\tJJJJJ\n"
)
expected_conseqs = {'test': 'ACAGGGAGACCC'}
conseqs = remap.sam_to_conseqs(sam_file)
self.assertDictEqual(expected_conseqs, conseqs)
def testComplexInsertion(self):
# Insertions are ignored if not a multiple of three
sam_file = StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M1I3M2I6M\t=\t1\t12\tACAGAGAGGCCCAAC\tJJJJJJJJJJJJJJJ\n"
)
expected_conseqs = {'test': 'ACAAGACCCAAC'}
conseqs = remap.sam_to_conseqs(sam_file)
self.assertDictEqual(expected_conseqs, conseqs)
def testReverseLeftOfForward(self):
sam_file = StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t2\t44\t1M\t=\t1\t1\tC\tJ\n"
"test1\t147\ttest\t1\t44\t1M\t=\t2\t-1\tA\tJ\n"
)
expected_conseqs = {'test': 'AC'}
conseqs = remap.sam_to_conseqs(sam_file)
self.assertDictEqual(expected_conseqs, conseqs)
def testAllLowQuality(self):
# SAM:qname, flag, rname, pos, mapq, cigar, rnext, pnext, tlen, seq, qual
sam_file = StringIO("@SQ\tSN:test\n"
"test1\t147\ttest\t1\t24\t1M\t=\t1\t-1\tT\t#\n")
expected_conseqs = {}
conseqs = remap.sam_to_conseqs(sam_file, quality_cutoff=32)
self.assertDictEqual(expected_conseqs, conseqs)
def testPairMapsToTwoReferences(self):
samIO = StringIO.StringIO(
"@SQ\tSN:testX\n"
"@SQ\tSN:testY\n"
"test1\t99\ttestX\t1\t44\t3M\t=\t1\t3\tACG\tJJJ\n"
"test1\t147\ttestY\t1\t44\t3M\t=\t1\t-3\tACG\tJJJ\n")
expected_conseqs = {}
conseqs = remap.sam_to_conseqs(samIO)
self.assertDictEqual(expected_conseqs, conseqs)
def testHeaders(self):
samIO = StringIO.StringIO(
"@SH\tsome header\n"
"@MHI\tmost headers are ignored, except SQ for sequence reference\n"
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M\t=\t1\t3\tACA\tJJJ\n")
expected_conseqs = {'test': 'ACA'}
conseqs = remap.sam_to_conseqs(samIO)
self.assertDictEqual(expected_conseqs, conseqs)
def testDeletionInSomeReads(self):
samIO = StringIO.StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M3D3M\t=\t3\t6\tACAGGG\tJJJJJJ\n"
"test2\t99\ttest\t1\t44\t3M3D3M\t=\t3\t6\tACAGGG\tJJJJJJ\n"
"test3\t99\ttest\t1\t44\t9M\t=\t3\t9\tACATTTGGG\tJJJJJJJJJ\n")
expected_conseqs = {'test': 'ACATTTGGG'}
conseqs = remap.sam_to_conseqs(samIO)
self.assertDictEqual(expected_conseqs, conseqs)
def testComplexInsertion(self):
# Insertions are ignored if not a multiple of three
samIO = StringIO.StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M1I3M2I6M\t=\t1\t12\tACAGAGAGGCCCAAC\tJJJJJJJJJJJJJJJ\n"
)
expected_conseqs = {'test': 'ACAAGACCCAAC'}
conseqs = remap.sam_to_conseqs(samIO)
self.assertDictEqual(expected_conseqs, conseqs)
def testSimple(self):
# SAM:qname, flag, rname, pos, mapq, cigar, rnext, pnext, tlen, seq, qual
samIO = StringIO.StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t12M\t=\t1\t12\tACAAGACCCAAC\tJJJJJJJJJJJJ\n"
)
expected_conseqs = {'test': 'ACAAGACCCAAC'}
conseqs = remap.sam_to_conseqs(samIO)
self.assertDictEqual(expected_conseqs, conseqs)
def testSeedsWithLowQuality(self):
samIO = StringIO.StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t4\t44\t3M\t=\t10\t3\tTAT\tJJ/\n")
seeds = {'test': 'ACATTTGGGCAC'}
expected_conseqs = {'test': 'ACATATGGGCAC'}
conseqs = remap.sam_to_conseqs(samIO, seeds=seeds, quality_cutoff=32)
self.assertDictEqual(expected_conseqs, conseqs)
def testMaxConsensus(self):
samIO = StringIO.StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M\t=\t1\t3\tACA\tJJJ\n"
"test2\t147\ttest\t1\t44\t3M\t=\t1\t-3\tACA\tJJJ\n"
"test3\t99\ttest\t1\t44\t3M\t=\t1\t3\tTCA\tJJJ\n"
)
expected_conseqs = {'test': 'ACA'}
conseqs = remap.sam_to_conseqs(samIO)
self.assertDictEqual(expected_conseqs, conseqs)
def testHeaders(self):
sam_file = StringIO(
"@SH\tsome header\n"
"@MHI\tmost headers are ignored, except SQ for sequence reference\n"
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M\t=\t1\t3\tACA\tJJJ\n"
)
expected_conseqs = {'test': 'ACA'}
conseqs = remap.sam_to_conseqs(sam_file)
self.assertDictEqual(expected_conseqs, conseqs)
def testLowQuality(self):
# Note that we ignore the overlapped portion of the reverse read,
# even if it has higher quality.
sam_file = StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M\t=\t1\t3\tACG\tJ/J\n"
)
expected_conseqs = {'test': 'ANG'}
conseqs = remap.sam_to_conseqs(sam_file, quality_cutoff=32)
self.assertDictEqual(expected_conseqs, conseqs)
def testDeletionInSomeReads(self):
sam_file = StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M3D3M\t=\t3\t6\tACAGGG\tJJJJJJ\n"
"test2\t99\ttest\t1\t44\t3M3D3M\t=\t3\t6\tACAGGG\tJJJJJJ\n"
"test3\t99\ttest\t1\t44\t9M\t=\t3\t9\tACATTTGGG\tJJJJJJJJJ\n"
)
expected_conseqs = {'test': 'ACATTTGGG'}
conseqs = remap.sam_to_conseqs(sam_file)
self.assertDictEqual(expected_conseqs, conseqs)
def testPairMapsToTwoReferences(self):
sam_file = StringIO(
"@SQ\tSN:testX\n"
"@SQ\tSN:testY\n"
"test1\t99\ttestX\t1\t44\t3M\t=\t1\t3\tACG\tJJJ\n"
"test1\t147\ttestY\t1\t44\t3M\t=\t1\t-3\tACG\tJJJ\n"
)
expected_conseqs = {}
conseqs = remap.sam_to_conseqs(sam_file)
self.assertDictEqual(expected_conseqs, conseqs)
def testLowQualityAndDeletion(self):
samIO = StringIO.StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M3D3M\t=\t3\t6\tACAGGG\tJJJJJJ\n"
"test2\t99\ttest\t1\t44\t9M\t=\t3\t9\tACATTTGGG\tJJJ///JJJ\n")
expected_conseqs = {'test': 'ACANNNGGG'}
conseqs = remap.sam_to_conseqs(samIO, quality_cutoff=32)
self.assertDictEqual(expected_conseqs, conseqs)
def testNothingMapped(self):
samIO = StringIO.StringIO("@SQ\tSN:test\tSN:other\n")
seeds = {'test': 'ATGAAGTACTCTCT', 'other': 'AAGCCGAAGTGTGT'}
expected_conseqs = {}
conseqs = remap.sam_to_conseqs(samIO,
seeds=seeds,
is_filtered=True,
filter_coverage=2)
self.assertDictEqual(expected_conseqs, conseqs)
def testAllLowQuality(self):
# SAM:qname, flag, rname, pos, mapq, cigar, rnext, pnext, tlen, seq, qual
sam_file = StringIO(
"@SQ\tSN:test\n"
"test1\t147\ttest\t1\t24\t1M\t=\t1\t-1\tT\t#\n"
)
expected_conseqs = {}
conseqs = remap.sam_to_conseqs(sam_file, quality_cutoff=32)
self.assertDictEqual(expected_conseqs, conseqs)
def testLowQualityAndDeletion(self):
sam_file = StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M3D3M\t=\t3\t6\tACAGGG\tJJJJJJ\n"
"test2\t99\ttest\t1\t44\t9M\t=\t3\t9\tACATTTGGG\tJJJ///JJJ\n"
)
expected_conseqs = {'test': 'ACANNNGGG'}
conseqs = remap.sam_to_conseqs(sam_file, quality_cutoff=32)
self.assertDictEqual(expected_conseqs, conseqs)
def testSeedsNeedSomeReads(self):
sam_file = StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t4\t44\t3M\t=\t10\t3\tTAT\tJJJ\n"
)
seeds = {'test': 'ACATTTGGGCAC',
'other': 'TATGCACCC'}
expected_conseqs = {'test': 'ACATATGGGCAC'}
conseqs = remap.sam_to_conseqs(sam_file, seeds=seeds)
self.assertDictEqual(expected_conseqs, conseqs)
def testSeeds(self):
samIO = StringIO.StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t4\t44\t3M\t=\t10\t3\tTAT\tJJJ\n"
"test2\t99\ttest\t10\t44\t3M\t=\t4\t-3\tCAC\tJJJ\n"
)
seeds = {'test': 'ACATTTGGGCAC'}
expected_conseqs = {'test': 'ACATATGGGCAC'}
conseqs = remap.sam_to_conseqs(samIO, seeds=seeds)
self.assertDictEqual(expected_conseqs, conseqs)
def testSeedsWithLowQuality(self):
sam_file = StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t4\t44\t3M\t=\t10\t3\tTAT\tJJ/\n"
)
seeds = {'test': 'ACATTTGGGCAC'}
expected_conseqs = {'test': 'ACATATGGGCAC'}
conseqs = remap.sam_to_conseqs(sam_file,
seeds=seeds,
quality_cutoff=32)
self.assertDictEqual(expected_conseqs, conseqs)
def testSeedsWithCodonDeletion(self):
sam_file = StringIO(
"@SQ\tSN:test\n"
"test1\t99\ttest\t1\t44\t3M3D3M\t=\t10\t6\tACAGGG\tJJJJJJ\n"
)
seeds = {'test': 'ACATTTGGGCAC'}
expected_conseqs = {'test': 'ACATTTGGGCAC'}
conseqs = remap.sam_to_conseqs(sam_file,
seeds=seeds,
quality_cutoff=32)
self.assertDictEqual(expected_conseqs, conseqs)
