def test_fix_donor_case3(self):
""" Toy transcript with sequence AAGGT|GAA, where the splice motif
is noncanonical but located 2 bp from a canonical splice donor.
chr1: 23,071,357 - 23,072,126
So-called case #3
"""
# Process references
sjFile = "input_files/test_junctions.txt"
tmp_dir = "scratch/test/TC_tmp/"
chroms = set(["chr1"])
donors, acceptors, sjDict = TC.processSpliceAnnotation(sjFile, tmp_dir,
chroms)
genome = Fasta("input_files/hg38_chr1.fa")
# Init transcript object
sam_fields = ["test_read", "0", "chr1", "23071357", "255", "5M762N3M", "*",
"0", "0", "AAGGTGAA", "*", "NM:i:0", "MD:Z:8"]
transcript = t2.Transcript(sam_fields, genome, sjDict)
jnNumber = 0
maxDist = 5
donor = (transcript.spliceJunctions[jnNumber]).bounds[0]
# Attempt to correct the splice donor side of the junction (left)
new_seq, new_cigar = TC.fix_one_side_of_junction(transcript.CHROM,
transcript.POS, jnNumber,
donor, -2, genome,
transcript.SEQ,
transcript.CIGAR)
assert new_seq == "AAGGAA"
assert new_cigar == "3M764N3M"
def test_update(self):
""" Toy transcript with sequence A|GAA, where the splice motif
is noncanonical but located 2 bp from a canonical splice donor.
chr1: 23,071,357 - 23,072,126
"""
# Process references
sjFile = "input_files/test_junctions.txt"
tmp_dir = "scratch/test/TC_tmp/"
chroms = set(["chr1"])
donor, acceptor, sjDict = TC.processSpliceAnnotation(
sjFile, tmp_dir, chroms)
genome = Fasta("input_files/hg38_chr1.fa")
# Init transcript object
sam_fields = [
"test_read", "0", "chr1", "23071357", "255", "1M766N3M", "*", "0",
"0", "AGAA", "*", "NM:i:0", "MD:Z:4"
]
transcript = t2.Transcript(sam_fields, genome, sjDict)
jnNumber = 0
maxDist = 5
donor = (transcript.spliceJunctions[jnNumber]).bounds[0]
# Attempt to correct the splice donor side of the junction (left)
transcript.SEQ, transcript.CIGAR = TC.fix_one_side_of_junction(
transcript.CHROM, transcript.POS, jnNumber, donor, 2, genome,
transcript.SEQ, transcript.CIGAR)
# Now test the update function
TC.update_post_ncsj_correction(transcript, jnNumber, genome, sjDict)
junction = transcript.spliceJunctions[jnNumber]
assert junction.motif_code == "21"
assert junction.isCanonical == True
assert transcript.MD == "MD:Z:6"
assert transcript.isCanonical == True
