def test_mismatch(self):
""" Compare SEQ and CIGAR for a spliced transcript that contains a
mismatch. """
sam = "input_files/sams/mismatch.sam"
genome = Fasta("input_files/hg38_chr1.fa")
sjDict = set()
with open(sam, 'r') as f:
sam_line = f.readline().strip().split('\t')
transcript = t2.Transcript(sam_line, genome, sjDict)
assert t2.check_seq_and_cigar_length(transcript.SEQ,
transcript.CIGAR) == True
def test_perfect_match_with_introns(self):
""" Compare SEQ and CIGAR for a transcript that is a perfect
reference match containing introns. """
sam = "input_files/sams/perfectReferenceMatch_twoIntrons.sam"
genome = Fasta("input_files/hg38_chr1.fa")
sjDict = set()
with open(sam, 'r') as f:
sam_line = f.readline().strip().split('\t')
transcript = t2.Transcript(sam_line, genome, sjDict)
assert t2.check_seq_and_cigar_length(transcript.SEQ,
transcript.CIGAR) == True
def test_perfect_match(self):
""" Since this read is a perfect match to the reference, its CIGAR and
sequence fields should definitely be the same length """
sam = "input_files/sams/perfectReferenceMatch_noIntrons.sam"
genome = Fasta("input_files/hg38_chr1.fa")
sjDict = set()
with open(sam, 'r') as f:
sam_line = f.readline().strip().split('\t')
transcript = t2.Transcript(sam_line, genome, sjDict)
assert t2.check_seq_and_cigar_length(transcript.SEQ,
transcript.CIGAR) == True
def test_insertion_deletion_mismatch_ncsj(self):
""" Compare SEQ and CIGAR for a transcript that contains an
insertion, deletion, mismatch, and noncanonical splice junction in
it. """
sam = "input_files/sams/deletion_insertion_mismatch_nc.sam"
genome = Fasta("input_files/hg38_chr1.fa")
sjDict = set()
with open(sam, 'r') as f:
sam_line = f.readline().strip().split('\t')
transcript = t2.Transcript(sam_line, genome, sjDict)
assert t2.check_seq_and_cigar_length(transcript.SEQ,
transcript.CIGAR) == True
def test_pre_correction_dmel(self):
""" This is a noisy Drosophila read, but prior to correction, the CIGAR
and SEQ strings should definitely match """
sam = "input_files/drosophila_example/input_read.sam"
genome = Fasta("input_files/drosophila_example/chr3R.fa")
sjDict = set()
with open(sam, 'r') as f:
for sam_line in f:
if sam_line.startswith("@"):
continue
else:
sam_line = sam_line.strip().split('\t')
transcript = t2.Transcript(sam_line, genome, sjDict)
assert t2.check_seq_and_cigar_length(transcript.SEQ,
transcript.CIGAR) == True
def test_not_matching(self):
""" This is the sam read as above but after correction with TCv2.0.1.
The read got flagged by samtools after correction as having
inconsistent CIGAR and SEQ fields """
sam = "input_files/drosophila_example/bad_correction.sam"
genome = Fasta("input_files/drosophila_example/chr3R.fa")
sjDict = set()
with open(sam, 'r') as f:
for sam_line in f:
if sam_line.startswith("@"):
continue
else:
sam_line = sam_line.strip().split('\t')
transcript = t2.Transcript(sam_line, genome, sjDict)
assert t2.check_seq_and_cigar_length(transcript.SEQ,
transcript.CIGAR) == False