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_variant_insertion(self):
""" Toy transcript with sequence AAATTGA, where the Ts are a 2 bp
insertion that matches a known variant.
chr1: 202,892,094 - 202,892,098. Insertion is between position
202,892,096 and 202,892,097. The genomic position used to refer
to it is 202,892,097 """
sam_fields = [
"test_read", "0", "chr1", "202892094", "255", "3M2I2M", "*", "0",
"0", "AAATTGA", "*", "NM:i:2", "MD:Z:5", "jI:B:i,-1", "jM:B:c,-1"
]
genome = Fasta("input_files/hg38_chr1.fa")
maxLen = 5
spliceAnnot = None
variants = {"chr1_202892096_202892098": "TT"}
logInfo = TC.init_log_info(sam_fields)
# Init transcript object
transcript = t2.Transcript(sam_fields, genome, spliceAnnot)
# Run correction
TE_entries = TC.correctInsertions(transcript, genome, variants, maxLen,
logInfo)
# Check to see if correction was successful
assert transcript.SEQ == "AAATTGA"
assert transcript.CIGAR == "3M2I2M"
# Check the log entries
expected_log = "\t".join([
"test_read", "chr1_202892096_202892098", "Insertion", "2",
"Uncorrected", "VariantMatch"
]) + "\n"
assert TE_entries == expected_log
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
def test_wrong_variant_mismatch(self):
""" Toy transcript with sequence AACGA, where the C is a mismatch to the
reference base 'A' in the location, but not matching, a known SNP.
chr1: 202,892,094 - 202,892,098. Mismatch is at 202,892,096 """
sam_fields = [
"test_read", "0", "chr1", "202892094", "255", "5M", "*", "0", "0",
"AACGA", "*", "NM:i:1", "MD:Z:2A2", "jI:B:i,-1", "jM:B:c,-1"
]
genome = Fasta("input_files/hg38_chr1.fa")
spliceAnnot = None
variants = {"chr1_202892096": ["G"]}
logInfo = TC.init_log_info(sam_fields)
# Init transcript object
transcript = t2.Transcript(sam_fields, genome, spliceAnnot)
# Run correction
error_entries = TC.correctMismatches(transcript, genome, variants,
logInfo)
# Check to see if correction was successful
assert transcript.SEQ == "AAAGA"
assert transcript.CIGAR == "5M"
# Check the number and content of the transcript error entries
assert error_entries.count('\n') == 1
assert "Corrected" in error_entries
assert "VariantMatch" not in error_entries
def test_two_mismatches(self):
""" Correct 2 mismatches in the same read. Useful for making sure that
the TE log string is correct. """
sam_fields = [
"test_read", "0", "chr1", "202892094", "255", "5M", "*", "0", "0",
"ACCGA", "*", "NM:i:2", "MD:Z:1A0A2", "jI:B:i,-1", "jM:B:c,-1"
]
genome = Fasta("input_files/hg38_chr1.fa")
spliceAnnot = None
variants = {}
logInfo = TC.init_log_info(sam_fields)
# Init transcript object
transcript = t2.Transcript(sam_fields, genome, spliceAnnot)
# Run correction
error_entries = TC.correctMismatches(transcript, genome, variants,
logInfo)
# Check to see if correction was successful
assert transcript.SEQ == "AAAGA"
assert transcript.CIGAR == "5M"
# Check the number and content of the transcript error entries
print(error_entries)
assert error_entries.count('\n') == 2
assert error_entries.count('Corrected') == 2
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
