def test_file_extension_deletion_success(self):
"""
Asserts that a pd.DataFrame is returned only if file extension matches.
"""
self.assertTrue(
isinstance(gi.file_extension(self.test_input2, 'deletion'),
pd.DataFrame))
def test_flanking_regions_fasta_insertion(self):
"""
Asserts that insertions are handled properly for both forward and reverse strand insertions.
"""
dataframe = gi.file_extension(self.insertion_input2, 'insertion')
flanking = gi.flanking_region_fasta_insertion(self.insertion_genome,
dataframe, 5)
self.assertTrue(len(flanking) == 8)
def test_match_chr_to_genome(self):
"""
Asserts that a pd.DataFrame object is returned from function.
chr format is mismatched between genome and input file, checks for conversion.
"""
dataframe = gi.file_extension(self.test_input2, 'deletion')
self.assertTrue(
isinstance(
gi.match_chr_to_genome(dataframe, self.genome, 'deletion'),
pd.DataFrame))
def test_flanking_regions_fasta_translocation(self):
"""
Asserts that translocations are handled properly for both forward and reverse strand translocations.
"""
dataframe = gi.file_extension(self.translocation_input2,
'translocation')
flanking = gi.flanking_region_fasta_translocation(
self.insertion_genome, dataframe, 5)
self.assertTrue(flanking[0][1] == 'CCAAAAATTT')
self.assertTrue(flanking[1][1] == 'AAAATAATTT')
self.assertTrue(flanking[2][1] == 'CCAAATTTTT')
self.assertTrue(flanking[3][1] == 'AAAATTTTTT')
def iterator_sv(args):
""" Use an input regions file with SV positions to pull
down flanking sequence on both sides of SV to generate
primers upstream and downstream of the SV.
Args:
args (Namespace): Argparse results.
Returns: None
"""
dataset_name = os.path.splitext(str(args.regions_file))[0]
genome = giv.genome_iterator(args.ref_genome)
# 2) create dataframe from input regions file
if args.sv in ('deletion', 'inversion'):
small_regions = giv.file_extension(args.regions_file, args.sv)
# 3) ensure proper proper number of columns in dataframe
assert len(list(small_regions)) == 5, "DataFrame contains more/less than 5 columns...\
Improper format."
# 4) format dataframe "chr" column to match reference genome
small_regions = giv.match_chr_to_genome(small_regions, genome, args.sv)
# 5) generate flanking regions fasta based on position in input file
flanking = open("flanking_regions.%s.fasta" % dataset_name, 'w')
if args.sv == 'deletion':
flank_data = giv.flanking_regions_fasta_deletion(genome, small_regions, args.flanking_region_size)
primer3_in = open("primer3_input.%s.txt" % dataset_name, 'w')
for head, seq in flank_data:
flanking.write(">"+head+'\n'+seq+'\n')
# 6) generate primer3 input file
primer3_in.write(utils.primer3_input(head, seq, args))
elif args.sv == 'inversion':
flank_data = giv.flanking_regions_fasta_inversion(genome, small_regions, args.flanking_region_size)
primer3_in = open("primer3_input.%s.txt" % dataset_name, 'w')
for head, seq in flank_data:
flanking.write(">"+head+'\n'+seq+'\n')
# 6) generate primer3 input file
primer3_in.write(utils.primer3_input(head, seq, args))
flanking.close()
primer3_in.close()
elif args.sv == 'insertion':
small_regions = giv.file_extension(args.regions_file, args.sv)
assert len(list(small_regions)) == 10, "DataFrame contains more/less than 10 columns... Exiting."
small_regions = giv.match_chr_to_genome(small_regions, genome, args.sv)
flanking = open("flanking_regions.%s.fasta" %dataset_name, 'w')
flank_data = giv.flanking_region_fasta_insertion(genome, small_regions, args.flanking_region_size)
primer3_in = open("primer3_input.%s.txt" % dataset_name, 'w')
for head, seq in flank_data:
flanking.write(">"+head+'\n'+seq+'\n')
primer3_in.write(utils.primer3_input(head, seq, args))
elif args.sv == 'translocation':
small_regions = giv.file_extension(args.regions_file, args.sv)
assert len(list(small_regions)) == 8, "DataFrame contains more/less than 8 columns... Exiting."
small_regions = giv.match_chr_to_genome(small_regions, genome, args.sv)
flanking = open("flanking_regions.%s.fasta" %dataset_name, 'w')
flank_data = giv.flanking_region_fasta_translocation(genome, small_regions, args.flanking_region_size)
primer3_in = open("primer3_input.%s.txt" %dataset_name, 'w')
for head, seq in flank_data:
flanking.write(">"+head+'\n'+seq+'\n')
primer3_in.write(utils.primer3_input(head, seq, args))
flanking.close()
primer3_in.close()
def test_file_extension_insertion_success(self):
"""
Asserts that proper df is created when sv type is insertion.
"""
self.assertEqual(
len(gi.file_extension(self.insertion_input1, 'insertion')), 4)