def test_wrong_variant_mismatch(self):
""" Toy transcript with sequence AACGA, where the C is a mismatch to the
reference base 'A' in the location, but not matching, a known SNP.
chr1: 202,892,094 - 202,892,098. Mismatch is at 202,892,096 """
sam_fields = [
"test_read", "0", "chr1", "202892094", "255", "5M", "*", "0", "0",
"AACGA", "*", "NM:i:1", "MD:Z:2A2", "jI:B:i,-1", "jM:B:c,-1"
]
genome = Fasta("input_files/hg38_chr1.fa")
spliceAnnot = None
variants = {"chr1_202892096": ["G"]}
logInfo = TC.init_log_info(sam_fields)
# Init transcript object
transcript = t2.Transcript(sam_fields, genome, spliceAnnot)
# Run correction
error_entries = TC.correctMismatches(transcript, genome, variants,
logInfo)
# Check to see if correction was successful
assert transcript.SEQ == "AAAGA"
assert transcript.CIGAR == "5M"
# Check the number and content of the transcript error entries
assert error_entries.count('\n') == 1
assert "Corrected" in error_entries
assert "VariantMatch" not in error_entries
def test_two_mismatches(self):
""" Correct 2 mismatches in the same read. Useful for making sure that
the TE log string is correct. """
sam_fields = [
"test_read", "0", "chr1", "202892094", "255", "5M", "*", "0", "0",
"ACCGA", "*", "NM:i:2", "MD:Z:1A0A2", "jI:B:i,-1", "jM:B:c,-1"
]
genome = Fasta("input_files/hg38_chr1.fa")
spliceAnnot = None
variants = {}
logInfo = TC.init_log_info(sam_fields)
# Init transcript object
transcript = t2.Transcript(sam_fields, genome, spliceAnnot)
# Run correction
error_entries = TC.correctMismatches(transcript, genome, variants,
logInfo)
# Check to see if correction was successful
assert transcript.SEQ == "AAAGA"
assert transcript.CIGAR == "5M"
# Check the number and content of the transcript error entries
print(error_entries)
assert error_entries.count('\n') == 2
assert error_entries.count('Corrected') == 2
