def test_correct_jn(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"
outprefix = "scratch/test_jns/"
tmp_dir = "scratch/test_jns/TC_tmp/"
chroms = set(["chr1"])
donors, acceptors, sjAnnot = 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, sjAnnot)
jnNumber = 0
maxDist = 5
#donor = (transcript.spliceJunctions[jnNumber]).bounds[0]
# Attempt to correct the splice junction
correction_status, reason, dist = TC.attempt_jn_correction(
transcript, jnNumber, genome, donors, acceptors, sjAnnot, maxDist)
assert correction_status == True
assert reason == "NA"
assert dist == 2
def test_crash(self):
""" This is a Drosophila junction that borders a small match preceded by
a 7 bp deletion. It is supposed to crash correction, which will result
in a categorization of 'Other' in the log """
# Process references
sjFile = "input_files/drosophila_example/chr3R_SJs.tsv"
outprefix = "scratch/dmel_crash/"
tmp_dir = "scratch/dmel_crash/TC_tmp/"
chroms = set(["chr3R"])
donors, acceptors, sjAnnot = TC.processSpliceAnnotation(
sjFile, tmp_dir, chroms)
genome = Fasta("input_files/drosophila_example/chr3R.fa")
# Init transcript object
sam_fields = [
"test_read", "0", "chr3R", "14890420", "255", "7M7D2M264N7M", "*",
"0", "0", "GATCAAACAACAAGTC", "*"
]
transcript = t2.Transcript(sam_fields, genome, sjAnnot)
jnNumber = 0
maxDist = 5
# Attempt to correct the splice junction
correction_status, reason, dist = TC.attempt_jn_correction(
transcript, jnNumber, genome, donors, acceptors, sjAnnot, maxDist)
assert correction_status == False
assert reason == "Other"
assert dist == 5
def test_too_far_away(self):
""" A case where the NCSJ should not be corrected because it is too far
away from the closest annotated junction relative to the maxDist
parameter.
Toy transcript with sequence A|GAA, where the splice motif
is noncanonical.
chr1: 23,071,357 - 23,072,126
"""
# Process references
sjFile = "input_files/test_junctions.txt"
tmp_dir = "scratch/test_jns/TC_tmp/"
chroms = set(["chr1"])
donors, acceptors, sjAnnot = 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:6"
]
transcript = t2.Transcript(sam_fields, genome, sjAnnot)
jnNumber = 0
maxDist = 1
correction_status, reason, dist = TC.attempt_jn_correction(
transcript, jnNumber, genome, donors, acceptors, sjAnnot, maxDist)
assert correction_status == False
assert reason == "TooFarFromAnnotJn"
assert dist == 2
