def test_sj_corr_off(self):
""" Splice reference provided, but correction set to off. Expected
behavior is to skip SJ ref initialization because it would be a
waste of time """
# Initialize options etc.
sam = "input_files/sams/perfectReferenceMatch_noIntrons.sam"
tmp_dir = "scratch/prep_refs/sj_off/TC_tmp/"
os.system("mkdir -p " + tmp_dir)
options = dstruct.Struct()
options.refGenome = "input_files/hg38_chr1.fa"
options.tmp_dir = tmp_dir
options.maxLenIndel = options.maxSJOffset = 5
options.correctSJs = "false"
options.variantFile = None
options.sjAnnotFile = "input_files/test_junctions.txt"
header, chroms, sam_chunks = TC.split_SAM(sam, 1)
refs = TC.prep_refs(options, sam_chunks[0], header)
# Check that variant dicts are empty
assert refs.snps == refs.insertions == refs.deletions == {}
# Check that SJ bedtools and annot lookup are empty
assert refs.donors == refs.acceptors == None
assert refs.sjAnnot == set()
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_variants(self):
""" A variant file is provided """
# Initialize options etc.
sam = "input_files/vcf_test/read_with_snps.sam"
tmp_dir = "scratch/prep_refs/variant/TC_tmp/"
os.system("mkdir -p " + tmp_dir)
options = dstruct.Struct()
options.refGenome = "input_files/hg38_chr11.fa"
options.tmp_dir = tmp_dir
options.maxLenIndel = options.maxSJOffset = 5
options.correctSJs = "false"
options.variantFile = "input_files/vcf_test/snps.vcf"
options.sjAnnotFile = None
header, chroms, sam_chunks = TC.split_SAM(sam, 1)
refs = TC.prep_refs(options, sam_chunks[0], header)
# Check that variant deletion and insertion dicts are empty
assert len(refs.insertions) == 0
assert len(refs.deletions) == 0
assert len(refs.snps) > 0
# Check that SJ bedtools and annot lookup are empty
assert refs.donors == refs.acceptors == None
assert refs.sjAnnot == set()
def test_sjs(self):
""" Genome and splice junction reference provided. Variant structs
should still be empty. """
# Initialize options etc.
sam = "input_files/sams/perfectReferenceMatch_noIntrons.sam"
tmp_dir = "scratch/prep_refs/sjs/TC_tmp/"
os.system("mkdir -p " + tmp_dir)
options = dstruct.Struct()
options.refGenome = "input_files/hg38_chr1.fa"
options.tmp_dir = tmp_dir
options.maxLenIndel = options.maxSJOffset = 5
options.correctSJs = "true"
options.variantFile = None
options.sjAnnotFile = "input_files/test_junctions.txt"
header, chroms, sam_chunks = TC.split_SAM(sam, 1)
refs = TC.prep_refs(options, sam_chunks[0], header)
# Check that variant dicts are empty
assert refs.snps == refs.insertions == refs.deletions == {}
# Check SJ bedtools and annot lookup
assert (refs.donors).count() == 3
assert (refs.acceptors).count() == 2 # Same acceptor appears in 2 jns
assert len(refs.sjAnnot) == 3
def test_genome_only(self):
""" Make sure that the prep_refs function works under the simplest
possible option setting: no variants or SJs provided. """
# Initialize options etc.
sam = "input_files/sams/perfectReferenceMatch_noIntrons.sam"
tmp_dir = "scratch/prep_refs/genome-only/TC_tmp/"
os.system("mkdir -p " + tmp_dir)
options = dstruct.Struct()
options.refGenome = "input_files/hg38_chr1.fa"
options.tmp_dir = tmp_dir
options.maxLenIndel = options.maxSJOffset = 5
options.correctSJs = "false"
options.variantFile = None
options.sjAnnotFile = None
header, chroms, sam_chunks = TC.split_SAM(sam, 1)
refs = TC.prep_refs(options, sam_chunks[0], header)
# Check that variant dicts are empty
assert refs.snps == refs.insertions == refs.deletions == {}
# Check that SJ bedtools and annot lookup are empty
assert refs.donors == refs.acceptors == None
assert refs.sjAnnot == set()
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
def make_novelty_type_struct(database, datasets):
""" Create a data structure where it is possible to look up whether a gene
or transcript belongs to a particular category of novelty"""
conn = sqlite3.connect(database)
conn.row_factory = sqlite3.Row
cursor = conn.cursor()
novelty_type = dstruct.Struct()
novelty_type.known_genes = set(
qutils.fetch_all_known_genes_detected(cursor, datasets))
novelty_type.antisense_genes = set(
qutils.fetch_antisense_genes(cursor, datasets))
novelty_type.intergenic_genes = set(
qutils.fetch_intergenic_novel_genes(cursor, datasets))
novelty_type.known_transcripts = set(
qutils.fetch_all_known_transcripts_detected(cursor, datasets))
novelty_type.ISM_transcripts = set(
qutils.fetch_all_ISM_transcripts(cursor, datasets))
novelty_type.ISM_prefix = set(
qutils.fetch_prefix_ISM_transcripts(cursor, datasets))
novelty_type.ISM_suffix = set(
qutils.fetch_suffix_ISM_transcripts(cursor, datasets))
novelty_type.NIC_transcripts = set(
qutils.fetch_NIC_transcripts(cursor, datasets))
novelty_type.NNC_transcripts = set(
qutils.fetch_NNC_transcripts(cursor, datasets))
novelty_type.antisense_transcripts = set(
qutils.fetch_antisense_transcripts(cursor, datasets))
novelty_type.intergenic_transcripts = set(
qutils.fetch_intergenic_transcripts(cursor, datasets))
novelty_type.genomic_transcripts = set(
qutils.fetch_genomic_transcripts(cursor, datasets))
conn.close()
return novelty_type
def test_DIM_nc(self):
""" Correct a transcript containing a deletion, insertion, mismatch,
and noncanonical splice junction """
# Initialize options etc.
sam = "input_files/sams/deletion_insertion_mismatch_nc.sam"
genome = Fasta("input_files/hg38_chr1.fa")
sjFile = "input_files/GM12878_SJs_chr1.tab"
tmp_dir = "scratch/example/TC_tmp/"
os.system("mkdir -p %s" % tmp_dir)
chroms = set(["chr1"])
donors, acceptors, sjAnnot = TC.processSpliceAnnotation(
sjFile, tmp_dir, chroms)
outfiles = dstruct.Struct()
outfiles.TElog = open(tmp_dir + "DIM_nc_clean.TE.log", 'w')
outfiles.sam = open(tmp_dir + "DIM_nc_clean.sam", 'w')
outfiles.fasta = open(tmp_dir + "DIM_nc_clean.fasta", 'w')
outfiles.log = open(tmp_dir + "DIM_nc_clean.log", 'w')
refs = dstruct.Struct()
refs.sjAnnot = sjAnnot
refs.genome = genome
refs.donors = donors
refs.acceptors = acceptors
refs.snps = {}
refs.deletions = {}
refs.insertions = {}
options = dstruct.Struct()
options.maxLenIndel = 5
options.maxSJOffset = 5
options.correctMismatches = "true"
options.correctIndels = "true"
options.correctSJs = "true"
options.primaryOnly = True
options.canonOnly = False
# Correct the transcript
with open(sam, 'r') as f:
transcripts = [f.readline().strip()]
TC.batch_correct(transcripts, options, refs, outfiles)
# Close the output files
for handle in outfiles.values():
handle.close()
# Expected transcript attributes post-correction
correct_CIGAR = ("12M1134N126M163N202M866N74M924N191M1777N127M2109N"
"157M88N159M932N633M274N117M7696N170M1215N629M938N"
"29M428N133M254N166M390N212M253N89M163N483M")
correct_MD = "MD:Z:3709"
correct_NM = "NM:i:0"
correct_jI = (
"jI:B:i,150941429,150942562,150942689,150942851,150943054,"
"150943919,150943994,150944917,150945109,150946885,150947013,"
"150949121,150949279,150949366,150949526,150950457,150951091,"
"150951364,150951482,150959177,150959348,150960562,150961192,"
"150962129,150962159,150962586,150962720,150962973,150963140,"
"150963529,150963742,150963994,150964084,150964246")
correct_jM = "jM:B:c,21,21,21,21,21,21,21,21,21,21,21,21,21,21,21,21,21"
# Read in transcript from outfile
with open(tmp_dir + "DIM_nc_clean.sam", 'r') as f:
sam_line = f.readline().strip().split('\t')
transcript = t2.Transcript(sam_line, genome, sjAnnot)
assert transcript.CIGAR == correct_CIGAR
assert transcript.MD == correct_MD
assert transcript.NM == correct_NM
assert transcript.jI == correct_jI
assert transcript.jM == correct_jM
# Read logs and make sure they are OK
expected_log = "\t".join([
"c34150/f1p1/3707", "primary", "2", "0", "0", "1", "0", "0", "2",
"0", "1", "0"
])
with open(tmp_dir + "DIM_nc_clean.log", 'r') as f:
log = f.readline().strip()
assert log == expected_log
