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_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_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()