def test_find_closest_splice_donor_minus(self):
""" For a toy case with multiple donors and acceptors in close
proximity, test whether TC can find the closest reference donor
to the supplied intron bound.
Similar to before, there is an exact match for the donor, located
at 23071360 in 1-based coordinates and 23071359 in 0-based."""
# Process reference junctions
sjFile = "input_files/test_junctions.txt"
tmp_dir = "scratch/test/TC_tmp/"
chroms = set(["chr1"])
donors, acceptors, sjDict = TC.processSpliceAnnotation(
sjFile, tmp_dir, chroms)
# Intron bound info
transcriptID = "test_read"
jnNumber = 0
chrom = "chr1"
start = 23070360
end = 23071360
strand = "-"
genome = Fasta("input_files/hg38_chr1.fa")
junction = sj.SpliceJunction(transcriptID, jnNumber, chrom, start, end,
strand, genome, sjDict)
donor = junction.get_splice_donor()
closest_donor = TC.find_closest_bound(donor, donors)
assert closest_donor.start == 23071359
assert closest_donor.end == 23071360
assert closest_donor.dist == 0
def test_find_closest_splice_acceptor_plus(self):
""" Find the closest splice acceptor, which is 17 bp upstream.
Plus strand."""
# Process reference junctions
sjFile = "input_files/test_junctions.txt"
tmp_dir = "scratch/test/TC_tmp/"
chroms = set(["chr1"])
donors, acceptors, sjDict = TC.processSpliceAnnotation(
sjFile, tmp_dir, chroms)
# Intron bound info
transcriptID = "test_read"
jnNumber = 0
chrom = "chr1"
start = 23071360
end = 23072140
strand = "+"
genome = Fasta("input_files/hg38_chr1.fa")
junction = sj.SpliceJunction(transcriptID, jnNumber, chrom, start, end,
strand, genome, sjDict)
acceptor = junction.get_splice_acceptor()
closest_acceptor = TC.find_closest_bound(acceptor, acceptors)
assert closest_acceptor.start == 23072122
assert closest_acceptor.end == 23072123
assert closest_acceptor.dist == -17
def test_find_closest_splice_acceptor_minus(self):
""" Find the closest splice acceptor, which is 1 bp downstream.
Minus strand. Note that dist is relative to the genome, not to
the direction of the transcript."""
# Process reference junctions
sjFile = "input_files/test_junctions.txt"
tmp_dir = "scratch/test/TC_tmp/"
chroms = set(["chr1"])
donors, acceptors, sjDict = TC.processSpliceAnnotation(
sjFile, tmp_dir, chroms)
# Intron bound info
transcriptID = "test_read"
jnNumber = 0
chrom = "chr1"
start = 22071331
end = 22073331
strand = "-"
genome = Fasta("input_files/hg38_chr1.fa")
junction = sj.SpliceJunction(transcriptID, jnNumber, chrom, start, end,
strand, genome, sjDict)
acceptor = junction.get_splice_acceptor()
closest_acceptor = TC.find_closest_bound(acceptor, acceptors)
assert closest_acceptor.start == 22071329
assert closest_acceptor.end == 22071330
assert closest_acceptor.dist == -1
