def test_noncanonical(self):
""" Transcript should be noncanonical and un-annotated prior to
correction, but be canonical and annotated afterwards """
sam = "input_files/sams/deletion_insertion_mismatch_nc.sam"
sjFile = "input_files/GM12878_SJs_chr1.tab"
tmp_dir = "scratch/test_jIjM/TC_tmp/"
chroms = set(["chr1"])
refs = dstruct.Struct()
refs.genome = Fasta("input_files/hg38_chr1.fa")
refs.donors, refs.acceptors, refs.sjAnnot = TC.processSpliceAnnotation(sjFile, tmp_dir,
chroms)
with open(sam, 'r') as f:
sam_line = f.readline().strip()
transcript, logInfo = TC.transcript_init(sam_line, refs.genome,
refs.sjAnnot)
assert transcript.allJnsAnnotated == False
assert transcript.isCanonical == False
# Now correct the junction and retest
upd_transcript, TE = TC.cleanNoncanonical(transcript, refs, 5, logInfo)
assert upd_transcript.allJnsAnnotated == True
assert upd_transcript.isCanonical == True
def test_crash_dmel(self):
""" This is a Drosophila junction that borders a small match preceded by
a 7 bp deletion. It is also supposed to crash correction, but did
not in TC v2.0.1."""
# Process references
sjFile = "input_files/drosophila_example/chr3R_SJs.tsv"
tmp_dir = "scratch/dmel/TC"
os.system("mkdir -p %s" % tmp_dir)
refs = dstruct.Struct()
chroms = set(["chr3R"])
refs.donors, refs.acceptors, refs.sjAnnot = TC.processSpliceAnnotation(
sjFile, tmp_dir, chroms)
refs.genome = Fasta("input_files/drosophila_example/chr3R.fa")
sam = "input_files/drosophila_example/no_SJ_corr.sam"
with open(sam, 'r') as f:
for sam_line in f:
if sam_line.startswith("@"):
continue
else:
sam_line = sam_line.strip().split('\t')
# Init transcript object
transcript = t2.Transcript(sam_line, refs.genome, refs.sjAnnot)
maxDist = 5
logInfo = TC.init_log_info(sam_line)
orig_CIGAR = transcript.CIGAR
orig_seq = transcript.SEQ
orig_MD = transcript.MD
expected_TE = "\t".join([
"m160713_133433_42182_c101000162550000001823232709161620_s1_p0/121139/11291_13013",
"chr3R_14890436_14890699", "NC_SJ_boundary", "5", "Uncorrected",
"Other"
]) + "\n"
assert transcript.isCanonical == False
# Attempt to correct the splice junction
new_transcript, TE_entries = TC.cleanNoncanonical(
transcript, refs, maxDist, logInfo)
print(TE_entries)
assert new_transcript.isCanonical == False
assert TE_entries == expected_TE
assert new_transcript.MD == orig_MD
assert logInfo.corrected_NC_SJs == 0
assert logInfo.uncorrected_NC_SJs == 1
assert new_transcript.CIGAR == orig_CIGAR
assert new_transcript.SEQ == orig_seq
def test_crash_correction(self):
""" This is a case that is supposed to crash the NCSJ correction process,
resulting in no correction. This is because the mapping has
created a 7-bp micro-exon with a canonical but likely incorrect
junction to its left, and a non-canonical junction on its right.
Post-correction, we end up with two introns next to each other
with a zero-length exon, which is not valid."""
# Process references
sjFile = "input_files/chr11_sjs.txt"
tmp_dir = "scratch/test/TC_tmp/"
os.system("mkdir -p %s" % tmp_dir)
refs = dstruct.Struct()
chroms = set(["chr11"])
refs.donors, refs.acceptors, refs.sjAnnot = TC.processSpliceAnnotation(
sjFile, tmp_dir, chroms)
refs.genome = Fasta("input_files/hg38_chr11.fa")
sam = "input_files/sams/microexon.sam"
with open(sam, 'r') as f:
sam_line = f.readline().strip().split('\t')
# Init transcript object
transcript = t2.Transcript(sam_line, refs.genome, refs.sjAnnot)
maxDist = 5
logInfo = TC.init_log_info(sam_line)
assert transcript.isCanonical == False
# Attempt to correct the splice junction
transcript, TE_entries = TC.cleanNoncanonical(transcript, refs,
maxDist, logInfo)
orig_CIGAR = ("1211M5612N57M464N30M2717N120M1097N23M2632N146M1225N"
"140M4770N72M5051N132M1513N87M567N142M3780N100M2160N"
"59M864N31M9891N69M1711N7M1341N47M13S")
assert transcript.isCanonical == False
assert transcript.MD == "MD:Z:2473"
assert logInfo.corrected_NC_SJs == 0
assert logInfo.uncorrected_NC_SJs == 1
assert transcript.CIGAR == orig_CIGAR
def test_correct_ncsj(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_ncsj/TC_tmp/"
os.system("mkdir -p %s" % tmp_dir)
refs = dstruct.Struct()
chroms = set(["chr1"])
refs.donors, refs.acceptors, refs.sjAnnot = TC.processSpliceAnnotation(
sjFile, tmp_dir, chroms)
refs.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, refs.genome, refs.sjAnnot)
jnNumber = 0
maxDist = 5
logInfo = TC.init_log_info(sam_fields)
assert transcript.isCanonical == False
# Attempt to correct the splice junction
transcript, TE_entries = TC.cleanNoncanonical(transcript, refs,
maxDist, logInfo)
assert transcript.isCanonical == True
assert transcript.spliceJunctions[jnNumber].isCanonical == True
assert transcript.SEQ == "AAGGAA"
assert transcript.CIGAR == "3M764N3M"
assert transcript.MD == "MD:Z:6"
assert logInfo.corrected_NC_SJs == 1