def test_not_correctable_deletion(self):
""" Same deletion again, but correction cutoff set to 0 """
sam_fields = [
"test_read", "0", "chr1", "202892094", "255", "2M1D2M", "*", "0",
"0", "AAGA", "*", "NM:i:1", "MD:Z:2^A2", "jI:B:i,-1", "jM:B:c,-1"
]
genome = Fasta("input_files/hg38_chr1.fa")
maxLen = 0
spliceAnnot = None
variants = {}
logInfo = TC.init_log_info(sam_fields)
# Init transcript object
transcript = t2.Transcript(sam_fields, genome, spliceAnnot)
# Run correction
TE_entries = TC.correctDeletions(transcript, genome, variants, maxLen,
logInfo)
# Check to see if correction was successful
assert transcript.SEQ == "AAGA"
assert transcript.CIGAR == "2M1D2M"
# Check TE log
expected_TE = "\t".join([
"test_read", "chr1_202892095_202892096", "Deletion", "1",
"Uncorrected", "TooLarge"
]) + "\n"
assert TE_entries == expected_TE
def test_variant_deletion(self):
""" Same deletion again, but with a matching variant at the same
location. Correct action is to leave the deletion in place """
sam_fields = [
"test_read", "0", "chr1", "202892094", "255", "2M1D2M", "*", "0",
"0", "AAGA", "*", "NM:i:1", "MD:Z:2^A2", "jI:B:i,-1", "jM:B:c,-1"
]
genome = Fasta("input_files/hg38_chr1.fa")
maxLen = 5
spliceAnnot = None
variants = {"chr1_202892095_202892096": 1}
logInfo = TC.init_log_info(sam_fields)
# Init transcript object
transcript = t2.Transcript(sam_fields, genome, spliceAnnot)
# Run correction
TE_entries = TC.correctDeletions(transcript, genome, variants, maxLen,
logInfo)
# Check to see if deletion is still there as expected
assert transcript.SEQ == "AAGA"
assert transcript.CIGAR == "2M1D2M"
# Check TE log
expected_TE = "\t".join([
"test_read", "chr1_202892095_202892096", "Deletion", "1",
"Uncorrected", "VariantMatch"
]) + "\n"
assert TE_entries == expected_TE
def test_correctable_deletion(self):
""" Toy transcript with sequence AA-GA, where the '-' is a deletion of
the base 'A'.
chr1: 202,892,094 - 202,892,098. Deletion is at 202,892,096 """
sam_fields = [
"test_read", "0", "chr1", "202892094", "255", "2M1D2M", "*", "0",
"0", "AAGA", "*", "NM:i:1", "MD:Z:2^A2", "jI:B:i,-1", "jM:B:c,-1"
]
genome = Fasta("input_files/hg38_chr1.fa")
maxLen = 5
spliceAnnot = None
variants = {}
logInfo = TC.init_log_info(sam_fields)
# Init transcript object
transcript = t2.Transcript(sam_fields, genome, spliceAnnot)
# Run correction
TE_entries = TC.correctDeletions(transcript, genome, variants, maxLen,
logInfo)
# Check to see if correction was successful
assert transcript.SEQ == "AAAGA"
assert transcript.CIGAR == "5M"
# Check TE log
expected_TE = "\t".join([
"test_read", "chr1_202892095_202892096", "Deletion", "1",
"Corrected", "NA"
]) + "\n"
assert TE_entries == expected_TE
