def test_oligo_generator__determine_oligo_from_block(self):
"""Tests that getting the oligo from block seq works.
"""
OLIGO_SIZE = 90
self.config.oligo_size = OLIGO_SIZE
OLIGO_END_BUFFER_DISTANCE = 20
self.config.oligo_end_buffer_distance = OLIGO_END_BUFFER_DISTANCE
# Ensures full space is explored
self.config.min_ss_dG = 100
# Ignore phosphorothioates for now.
self.config.num_phosphorothioate_bonds = 0
oligo_generator = OligoGenerator(self.config)
# Use seq cenetered aroud position 2216229.
REF = 'C'
UPSTREAM_OF_MUT = 'AACAACCAGCGCCACAGCGGATGCGTGGAGATTCGGCGGATGGCATCGCTACAGGCCAGCAATGCCAG'
DOWNSTREAM_OF_MUT = 'GCCGCAGCCAGCCAGAAACCACTGCCGAGGCTGGTACGCGCCAGCGCACTGCCATTTTGCGCCAGTTGG'
BLOCK_SEQ = UPSTREAM_OF_MUT + REF + DOWNSTREAM_OF_MUT
best_oligo_candidate, midpoint_range_explored = (
oligo_generator.determine_oligo_from_block(BLOCK_SEQ))
# Assert that we explored the full space (100 min dG ensures this.)
# NOTE: We are aware we miss one, but okay with it for simplicity.
EXPECTED_MIDPOINT_RANGE = [45, len(BLOCK_SEQ) - 44]
self.assertEqual(EXPECTED_MIDPOINT_RANGE, midpoint_range_explored)
def print_mage_oligos(variant_set,
output_filehandle,
target_id_prefix,
replication_origin_params,
experiment_dir=OPT_MAGE_EXPERIMENT_DIR__FORWARD):
"""Prints MAGE oligos for Variants in variant_set.
Args:
variant_set: A VariantSet.
output_filehandle: Target for writing the designed oligos.
target_id_prefix: String prefix used for target id string in output.
replication_origin_params: ReplicationOriginParams object.
experiment_dir: Direction to print oligos. Choose from VALID_PRINT_OLIGOS_DIR.
Raises:
ValidationException
"""
assert experiment_dir in OPT_MAGE_VALID_EXPERIMENT_DIRS
# First validate that we support printing oligos for this type.
passing_variants = _validate_variant_set_for_printing_mage_oligos(
variant_set)
config = OptMAGEConfig()
config.replication_origin = replication_origin_params.get_origin_interval()
config.replication_terminus = (
replication_origin_params.get_terminus_interval())
oligo_target_list = []
for variant in passing_variants:
alt_value = variant.variantalternate_set.all()[0].alt_value
# Configure the oligo for this variant.
target_params = {
'target_id': variant.position,
'strand': 1,
'start': variant.position,
'end': variant.position + 1,
}
if experiment_dir == OPT_MAGE_EXPERIMENT_DIR__REVERSE:
target_params.update({
'mutation_type':
OPT_MAGE_MUTATION_TYPE__REFERENCE,
})
else:
target_params.update({
'mutation_type': OPT_MAGE_MUTATION_TYPE__SUBSTITUTION,
'mutation_seq': alt_value,
})
oligo_target_list.append(OligoTarget(config, target_params))
oligo_generator = OligoGenerator(config)
oligo_result_list = [
oligo_generator.generate_oligo(oligo_target)
for oligo_target in oligo_target_list
]
OligoWriter.write_default(oligo_result_list, output_filehandle)
def print_mage_oligos(variant_set, output_filehandle, target_id_prefix,
replication_origin_params,
experiment_dir=OPT_MAGE_EXPERIMENT_DIR__FORWARD):
"""Prints MAGE oligos for Variants in variant_set.
Args:
variant_set: A VariantSet.
output_filehandle: Target for writing the designed oligos.
target_id_prefix: String prefix used for target id string in output.
replication_origin_params: ReplicationOriginParams object.
experiment_dir: Direction to print oligos. Choose from VALID_PRINT_OLIGOS_DIR.
Raises:
ValidationException
"""
assert experiment_dir in OPT_MAGE_VALID_EXPERIMENT_DIRS
# First validate that we support printing oligos for this type.
passing_variants = _validate_variant_set_for_printing_mage_oligos(
variant_set)
config = OptMAGEConfig()
config.replication_origin = replication_origin_params.get_origin_interval()
config.replication_terminus = (
replication_origin_params.get_terminus_interval())
oligo_target_list = []
for variant in passing_variants:
alt_value = variant.variantalternate_set.all()[0].alt_value
# Configure the oligo for this variant.
target_params = {
'target_id': variant.position,
'strand': 1,
'start': variant.position,
'end': variant.position + 1,
}
if experiment_dir == OPT_MAGE_EXPERIMENT_DIR__REVERSE:
target_params.update({
'mutation_type': OPT_MAGE_MUTATION_TYPE__REFERENCE,
})
else:
target_params.update({
'mutation_type': OPT_MAGE_MUTATION_TYPE__SUBSTITUTION,
'mutation_seq': alt_value,
})
oligo_target_list.append(OligoTarget(config, target_params))
oligo_generator = OligoGenerator(config)
oligo_result_list = [
oligo_generator.generate_oligo(oligo_target)
for oligo_target in oligo_target_list]
OligoWriter.write_default(oligo_result_list, output_filehandle)
def test_free_energy_optmization(self):
"""Tests that the oligo search optimizes the free energy and scans
both left and right of the mutation midpoint.
"""
self.config.should_calc_replichore = False
OLIGO_SIZE = 20
self.config.oligo_size = OLIGO_SIZE
OLIGO_END_BUFFER_DISTANCE = 2
self.config.oligo_end_buffer_distance = OLIGO_END_BUFFER_DISTANCE
OLIGO_GENERATOR = OligoGenerator(self.config)
### Test that the window slides downstream.
RAW_SEQ_1 = 'GGGGGGGGGGCCCCCCCCCCCCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA'
SEQ_OBJ_1 = Seq(RAW_SEQ_1, generic_dna)
GENOME_RECORD_1 = SeqRecord(SEQ_OBJ_1)
self.config.genome_record = GENOME_RECORD_1
OLIGO_TARGET = OligoTarget(
self.config, {
'target_id': '1',
'replichore': 2,
'strand': -1,
'start': 35,
'end': 36,
'mutation_type': 'R'
})
oligo_result = OLIGO_GENERATOR.generate_oligo(OLIGO_TARGET)
self.assertTrue(oligo_result.ss_dG > DEFAULT_MIN_SS_DG)
EXPECTED_SEQ = 'A*A*AAAAAAAAAAAAAAAAAA'
self.assertEqual(EXPECTED_SEQ, str(oligo_result.oligo_seq).upper())
### Test that the window slides upstream.
RAW_SEQ_2 = 'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGCCCCCCCCCCCCC'
SEQ_OBJ_2 = Seq(RAW_SEQ_2, generic_dna)
GENOME_RECORD_2 = SeqRecord(SEQ_OBJ_2)
self.config.genome_record = GENOME_RECORD_2
OLIGO_TARGET = OligoTarget(
self.config, {
'target_id': '1',
'replichore': 2,
'strand': -1,
'start': 22,
'end': 23,
'mutation_type': 'R'
})
oligo_result = OLIGO_GENERATOR.generate_oligo(OLIGO_TARGET)
self.assertTrue(oligo_result.ss_dG > DEFAULT_MIN_SS_DG)
EXPECTED_SEQ = 'A*A*AAAAAAAAAAAAAAAAAA'
self.assertEqual(EXPECTED_SEQ, str(oligo_result.oligo_seq).upper())
def test_mutation__positive_strand(self):
"""Test making a mutation relative to the positive strand.
"""
self.config.should_calc_replichore = False
OLIGO_SIZE = 7
self.config.oligo_size = OLIGO_SIZE
OLIGO_END_BUFFER_DISTANCE = 0
self.config.oligo_end_buffer_distance = OLIGO_END_BUFFER_DISTANCE
self.config.num_phosphorothioate_bonds = 0
self.config.min_ss_dG = -200 # just want the centered window
OLIGO_GENERATOR = OligoGenerator(self.config)
RAW_SEQ_1 = 'CGCTAGCCC'
SEQ_OBJ_1 = Seq(RAW_SEQ_1, generic_dna)
GENOME_RECORD_1 = SeqRecord(SEQ_OBJ_1)
self.config.genome_record = GENOME_RECORD_1
OLIGO_TARGET = OligoTarget(
self.config,
{
'target_id': '1',
'replichore': 2, # so we get an oligo in the positive sense.
'strand': 1,
'start': 4,
'end': 7,
'mutation_type': 'M',
'mutation_seq': 'TAA'
})
oligo_result = OLIGO_GENERATOR.generate_oligo(OLIGO_TARGET)
self.assertEqual(OLIGO_SIZE, len(oligo_result.oligo_seq))
self.assertEqual('TAG', str(oligo_result.original_seq))
self.assertEqual('TAA', str(oligo_result.mutation_seq))
EXPECTED_OLIGO_SEQ = 'GCTAACC'
self.assertEqual(EXPECTED_OLIGO_SEQ,
str(oligo_result.oligo_seq).upper())
# Try similar with oligo size 8.
OLIGO_SIZE = 8
self.config.oligo_size = OLIGO_SIZE
oligo_result = OLIGO_GENERATOR.generate_oligo(OLIGO_TARGET)
self.assertEqual(OLIGO_SIZE, len(oligo_result.oligo_seq))
EXPECTED_OLIGO_SEQ = 'CGCTAACC'
self.assertEqual(EXPECTED_OLIGO_SEQ,
str(oligo_result.oligo_seq).upper())
def test_input_accepts_strings_or_numbers(self):
"""Input might be parsed from file so should handle numbers as
strings.
"""
self.config.num_phosphorothioate_bonds = 0
OLIGO_GENERATOR = OligoGenerator(self.config)
OLIGO_TARGET = OligoTarget(
self.config,
{
'target_id': '1',
'replichore': 2, # so we get an oligo in the positive sense.
'strand': 1,
'start': '2216229', # Testing this.
'end': 2216230,
'mutation_type': 'M',
'mutation_seq': 'T'
})
OLIGO_GENERATOR.generate_oligo(OLIGO_TARGET)
def test_oligo_generator__from_reference__target_reverse_strand(self):
"""Test for synthesizing an oligo that targets the reverse strand,
meaning a forward-sense oligo.
"""
OLIGO_SIZE = 90
self.config.oligo_size = OLIGO_SIZE
OLIGO_END_BUFFER_DISTANCE = 20
self.config.oligo_end_buffer_distance = OLIGO_END_BUFFER_DISTANCE
# Set this arbitrarily low so we pretty much guarantee we get the
# oligo sequence centered around the mutation.
self.config.min_ss_dG = -200
# Ignore phosphorothioates for now.
self.config.num_phosphorothioate_bonds = 0
oligo_generator = OligoGenerator(self.config)
# Replichore 1 and positive strand means the anti-sense strand will
# be targeted, so the oligo will have a positive sense.
params = {
'target_id': 'r_1_set1_ftsA_104352',
'replichore': 'NA',
'strand': '+1',
'start': 104352,
'end': 104353,
'mutation_type': 'R'
}
oligo_target = OligoTarget(self.config, params)
# Test getting the candidate block sequence.
formatted_block_seq = str(
oligo_generator.get_candidate_block_seq(oligo_target)).upper()
EXPECTED_BLOCK_SEQ = 'CCGGATTCTTGATCCCTTCCTGATAGTCAATCGCATACTCTTGCGGGATCACATGCAGCACACGATGCTCATCGCGCACACGCACCGATTTCGCGGTATGGACGACGTTTTCCACATCTTCTTGCGTCACTTCTTCTT'
self.assertEqual(EXPECTED_BLOCK_SEQ, formatted_block_seq)
# Test getting the actual oligo seq.
formatted_oligo_seq = str(
oligo_generator.generate_oligo(oligo_target).oligo_seq).upper()
EXPECTED_OLIGO_SEQ = 'AGTCAATCGCATACTCTTGCGGGATCACATGCAGCACACGATGCTCATCGCGCACACGCACCGATTTCGCGGTATGGACGACGTTTTCCA'
self.assertEqual(OLIGO_SIZE, len(formatted_oligo_seq))
self.assertEqual(EXPECTED_OLIGO_SEQ, formatted_oligo_seq)
def test_mutation__full_genome__positive_strand(self):
self.config.num_phosphorothioate_bonds = 0
OLIGO_GENERATOR = OligoGenerator(self.config)
OLIGO_TARGET = OligoTarget(
self.config,
{
'target_id': '1',
'replichore': 2, # so we get an oligo in the positive sense.
'strand': 1,
'start': 2216229,
'end': 2216230,
'mutation_type': 'M',
'mutation_seq': 'T'
})
oligo_result = OLIGO_GENERATOR.generate_oligo(OLIGO_TARGET)
self.assertEqual(DEFAULT_OLIGO_SIZE, len(oligo_result.oligo_seq))
self.assertEqual('C', str(oligo_result.original_seq).upper())
self.assertEqual('T', str(oligo_result.mutation_seq).upper())
self.assertEqual(2216229, oligo_result.start)
self.assertEqual(2216230, oligo_result.end)
def test_oligo_generator__get_candidate_block_seq(self):
"""Tests the part of the mage generator that determines the candidate
block seq.
"""
OLIGO_SIZE = 90
self.config.oligo_size = OLIGO_SIZE
OLIGO_END_BUFFER_DISTANCE = 20
self.config.oligo_end_buffer_distance = OLIGO_END_BUFFER_DISTANCE
# Set this arbitrarily low so we pretty much guarantee we get the
# oligo sequence centered around the mutation.
self.config.min_ss_dG = -200
# Ignore phosphorothioates for now.
self.config.num_phosphorothioate_bonds = 0
oligo_generator = OligoGenerator(self.config)
# Replichore 1 and negative strand means the anti-sense strand will
# be targeted, so the oligo will have a positive sense.
REF = 'C'
params = {
'target_id': 'test',
'replichore': 'NA',
'strand': '+1',
'start': 2216229,
'end': 2216230,
'mutation_type': 'R'
}
oligo_target = OligoTarget(self.config, params)
# Test getting the candidate block sequence.
formatted_block_seq = str(
oligo_generator.get_candidate_block_seq(oligo_target)).upper()
UPSTREAM_OF_MUT = 'CAACAACCAGCGCCACAGCGGATGCGTGGAGATTCGGCGGATGGCATCGCTACAGGCCAGCAATGCCAG'
DOWNSTREAM_OF_MUT = 'GCCGCAGCCAGCCAGAAACCACTGCCGAGGCTGGTACGCGCCAGCGCACTGCCATTTTGCGCCAGTTG'
EXPECTED_BLOCK_SEQ = UPSTREAM_OF_MUT + REF + DOWNSTREAM_OF_MUT
self.assertEqual(len(EXPECTED_BLOCK_SEQ), len(formatted_block_seq))
self.assertEqual(EXPECTED_BLOCK_SEQ, formatted_block_seq)
def test_determine_oligo_sense(self):
"""Tests for OligoGenerator.determine_oligo_sense().
"""
OLIGO_GENERATOR = OligoGenerator(self.config)
# Replichore = 1, strand = +1.
self.assertEqual(
-1,
OLIGO_GENERATOR.determine_oligo_sense(
OligoTarget(
self.config, {
'target_id': 'r_1_set1_ftsA_104352',
'replichore': 'NA',
'strand': '+1',
'start': 104352,
'end': 104353,
'mutation_type': 'R'
})))
# Replichore = 1, strand = -1.
self.assertEqual(
-1,
OLIGO_GENERATOR.determine_oligo_sense(
OligoTarget(
self.config, {
'target_id': 'r_8_set1_surA_53597',
'replichore': 'NA',
'strand': '-1',
'start': 53597,
'end': 53598,
'mutation_type': 'R'
})))
# Replichore = 2, strand = +1.
self.assertEqual(
1,
OLIGO_GENERATOR.determine_oligo_sense(
OligoTarget(
self.config, {
'target_id': 'r_102_set5_csiR_2794168',
'replichore': 'NA',
'strand': +1,
'start': 2794168,
'end': 2794169,
'mutation_type': 'R'
})))
# Replichore = 2, strand = -1.
self.assertEqual(
1,
OLIGO_GENERATOR.determine_oligo_sense(
OligoTarget(
self.config, {
'target_id': 'r_3_set1_der_2635317',
'replichore': 'NA',
'strand': -1,
'start': 2635317,
'end': 2635318,
'mutation_type': 'R'
})))
def test_deletion(self):
"""Test making a deletion.
"""
self.config.should_calc_replichore = False
OLIGO_SIZE = 7
self.config.oligo_size = OLIGO_SIZE
OLIGO_END_BUFFER_DISTANCE = 2
self.config.oligo_end_buffer_distance = OLIGO_END_BUFFER_DISTANCE
self.config.num_phosphorothioate_bonds = 0
self.config.min_ss_dG = -200 # just want the centered window
OLIGO_GENERATOR = OligoGenerator(self.config)
# TCGC AGC
RAW_SEQ_1 = 'TTTTTTTCGCTAGCCCTTTTTTTTTTTTTTTT'
SEQ_OBJ_1 = Seq(RAW_SEQ_1, generic_dna)
GENOME_RECORD_1 = SeqRecord(SEQ_OBJ_1)
self.config.genome_record = GENOME_RECORD_1
OLIGO_TARGET = OligoTarget(
self.config,
{
'target_id': '1',
'replichore': 2, # so we get an oligo in the positive sense.
'strand': 1,
'start': 11,
'end': 12,
'mutation_type': 'D',
})
oligo_result = OLIGO_GENERATOR.generate_oligo(OLIGO_TARGET)
self.assertEqual(OLIGO_SIZE, len(oligo_result.oligo_seq))
EXPECTED_OLIGO_SEQ = 'TCGCAGC'
EXPECTED_OLIGO_SEQ_ALTERNATE = 'CGCAGCC'
self.assertTrue(
str(oligo_result.oligo_seq).upper()
in [EXPECTED_OLIGO_SEQ, EXPECTED_OLIGO_SEQ_ALTERNATE],
'Got: ' + str(oligo_result.oligo_seq).upper())
# Try similar with oligo size 8.
OLIGO_SIZE = 8
self.config.oligo_size = OLIGO_SIZE
oligo_result = OLIGO_GENERATOR.generate_oligo(OLIGO_TARGET)
self.assertEqual(OLIGO_SIZE, len(oligo_result.oligo_seq))
EXPECTED_OLIGO_SEQ = 'TCGCAGCC'
EXPECTED_OLIGO_SEQ_ALTERNATE = 'TTCGCAGC'
self.assertTrue(
str(oligo_result.oligo_seq).upper() in
[EXPECTED_OLIGO_SEQ, EXPECTED_OLIGO_SEQ_ALTERNATE])
### Test bigger deletion.
OLIGO_SIZE = 7
self.config.oligo_size = OLIGO_SIZE
OLIGO_TARGET = OligoTarget(
self.config,
{
'target_id': '1',
'replichore': 2, # so we get an oligo in the positive sense.
'strand': 1,
'start': 11,
'end': 14,
'mutation_type': 'D',
})
oligo_result = OLIGO_GENERATOR.generate_oligo(OLIGO_TARGET)
self.assertEqual(OLIGO_SIZE, len(oligo_result.oligo_seq))
EXPECTED_OLIGO_SEQ = 'TCGCCCC'
EXPECTED_OLIGO_SEQ_ALTERNATE = 'TTCGCCC'
self.assertTrue(
str(oligo_result.oligo_seq).upper() in
[EXPECTED_OLIGO_SEQ, EXPECTED_OLIGO_SEQ_ALTERNATE])
# Try similar with oligo size 8.
OLIGO_SIZE = 8
self.config.oligo_size = OLIGO_SIZE
oligo_result = OLIGO_GENERATOR.generate_oligo(OLIGO_TARGET)
self.assertEqual(OLIGO_SIZE, len(oligo_result.oligo_seq))
EXPECTED_OLIGO_SEQ = 'TTCGCCCC'
EXPECTED_OLIGO_SEQ_ALTERNATE = 'TCGCCCCT'
self.assertTrue(
str(oligo_result.oligo_seq).upper() in
[EXPECTED_OLIGO_SEQ, EXPECTED_OLIGO_SEQ_ALTERNATE])