def init_genome_camv(pseudo_targets):
""" Initializes the CaMV genome object for simulation
Args:
pseudo_targets: list of format [t1, t2, ..., tn]
where each is a dict with = {'label': ,
'target_sequence': ,
'target_start_idx': ,
'complex_concentration': ,
'sense': ,
'direction': ,
'domain_label': }
Returns:
complete Genome instance corresponding to CaMV with targets
"""
# initialize camv genome
sequence = convert_fasta_to_string("genome_camv.fasta")
genome_camv = Genome(sequence)
# initialize camv genome domains
#ncr_left_of_35S = ...
#genome_camv.add_domain(ncr_left_of_35S)
#ncr_right_of_35S = ...
#genome_camv.add_domain(ncr_right_of_35S)
#promoter_35S = ...
#genome_camv.add_domain(promoter_35S)
#promoter_19S = ...
#genome_camv.add_domain(promoter_19S)
#gene_P1 = ...
#genome_camv.add_domain(gene_P1)
#gene_P2 = ...
#genome_camv.add_domain(gene_P2)
#gene_P3 = ...
#genome_camv.add_domain(gene_P3)
#gene_P4 = ...
#genome_camv.add_domain(gene_P4)
#gene_P5 = ...
#genome_camv.add_domain(gene_P5)
gene_P6 = Domain("gene_P6", 500, 600, "orf", genome_camv)
genome_camv.add_domain(gene_P6)
# initialize camv genome targets
domain_labels = genome_camv.domains.keys()
for pseudo_target in pseudo_targets:
assert pseudo_target.domain_label in domain_labels
for domain_label in domain_labels:
if pseudo_target.domain_label == domain_label:
domain = genome_camv.domains[domain_label]
target = Target(pseudo_target['label'],
pseudo_target['target_sequence'],
pseudo_target['target_sequence'],
pseudo_target['target_start_idx'],
pseudo_target['complex_concentration'],
pseudo_target['sense'],
pseudo_target['direction'],
domain)
domain.add_target(target)
""" isaac's testing block
target_P6_1 = Target("P6_1", "ggagaaagaaaagatatttaaaa", "ggagaaagaaaagatatttaaaa", 521, complex_concentration, 1, 1, gene_P6)
print P6_1.grna
print P6.target_location("P6_1")
print P6_1.cut_probability
P6_1.cut()
P6_1.repair(dt)
print P6_1.sequence
print P6.target_location("P6_1")
print P6_1.cut_probability
print P6_1.shift
"""
return genome_camv
def init_genome_camv(pseudo_targets):
""" Initializes the CaMV genome object for simulation
Args:
pseudo_targets: list of format [t1, t2, ..., tn]
where each is a dict with = {'label': ,
'target_sequence': ,
'target_start_idx': ,
'complex_concentration': ,
'sense': ,
'direction': ,
'domain_label': }
Returns:
complete Genome instance corresponding to CaMV with targets
"""
# initialize camv genome
sequence = convert_fasta_to_string("genome_camv.fasta")
genome_camv = Genome(sequence)
# initialize camv genome domains
#ncr_left_of_35S = ...
#genome_camv.add_domain(ncr_left_of_35S)
#ncr_right_of_35S = ...
#genome_camv.add_domain(ncr_right_of_35S)
#promoter_35S = ...
#genome_camv.add_domain(promoter_35S)
#promoter_19S = ...
#genome_camv.add_domain(promoter_19S)
#gene_P1 = ...
#genome_camv.add_domain(gene_P1)
#gene_P2 = ...
#genome_camv.add_domain(gene_P2)
#gene_P3 = ...
#genome_camv.add_domain(gene_P3)
#gene_P4 = ...
#genome_camv.add_domain(gene_P4)
#gene_P5 = ...
#genome_camv.add_domain(gene_P5)
gene_P6 = Domain("gene_P6", 500, 600, "orf", genome_camv)
genome_camv.add_domain(gene_P6)
# initialize camv genome targets
domain_labels = genome_camv.domains.keys()
for pseudo_target in pseudo_targets:
assert pseudo_target.domain_label in domain_labels
for domain_label in domain_labels:
if pseudo_target.domain_label == domain_label:
domain = genome_camv.domains[domain_label]
target = Target(pseudo_target['label'],
pseudo_target['target_sequence'],
pseudo_target['target_sequence'],
pseudo_target['target_start_idx'],
pseudo_target['complex_concentration'],
pseudo_target['sense'],
pseudo_target['direction'], domain)
domain.add_target(target)
""" isaac's testing block
target_P6_1 = Target("P6_1", "ggagaaagaaaagatatttaaaa", "ggagaaagaaaagatatttaaaa", 521, complex_concentration, 1, 1, gene_P6)
print P6_1.grna
print P6.target_location("P6_1")
print P6_1.cut_probability
P6_1.cut()
P6_1.repair(dt)
print P6_1.sequence
print P6.target_location("P6_1")
print P6_1.cut_probability
print P6_1.shift
"""
return genome_camv
def init_genome_camv(pseudo_targets):
""" Initializes the CaMV genome object for simulation
Args:
pseudo_targets: list of format [t1, t2, ..., tn]
where each is a dict with = {'label': ,
'target_sequence': ,
'target_start_idx': ,
'complex_concentration': ,
'sense': ,
'domain_label': }
Returns:
complete Genome instance corresponding to CaMV with targets
"""
# initialize camv genome
sequence = convert_fasta_to_string("genome_camv.fasta")
genome_camv = Genome(sequence)
# gene coordinates from http://www.ncbi.nlm.nih.gov/nuccore/9626938
# initialize camv genome
#untracked_small = Domain("untracked_small", 5674, 5775, "untracked", genome_camv) # removing for now, overlaps 19s
#genome_camv.add_domain(untracked_small)
#untracked_large = Domain("untracked_large", 7436, 8024, "untracked", genome_camv)
#genome_camv.add_domain(untracked_large)
untracked_large = Domain("untracked_large", 7436, 363, "untracked", genome_camv)
genome_camv.add_domain(untracked_large)
promoter_35S = Domain("promoter_35S", 7092, 7435, "promoter", genome_camv)
genome_camv.add_domain(promoter_35S)
promoter_19S = Domain("promoter_19S", 5380, 5773, "promoter", genome_camv)
genome_camv.add_domain(promoter_19S)
gene_P1 = Domain("gene_P1", 364, 1347, "orf", genome_camv, promoter=promoter_35S)
genome_camv.add_domain(gene_P1)
gene_P2 = Domain("gene_P2", 1349, 1828, "orf", genome_camv, promoter=promoter_35S)
genome_camv.add_domain(gene_P2)
gene_P3 = Domain("gene_P3", 1830, 2219, "orf", genome_camv, promoter=promoter_35S)
genome_camv.add_domain(gene_P3)
gene_P4 = Domain("gene_P4", 2201, 3670, "orf", genome_camv, promoter=promoter_35S)
genome_camv.add_domain(gene_P4)
gene_P5 = Domain("gene_P5", 3633, 5672, "orf", genome_camv, promoter=promoter_35S)
genome_camv.add_domain(gene_P5)
gene_P6 = Domain("gene_P6", 5776, 7338, "orf", genome_camv, promoter=promoter_19S)
genome_camv.add_domain(gene_P6)
# initialize camv genome targets
domain_labels = genome_camv.domains.keys()
for pseudo_target in pseudo_targets:
assert pseudo_target["domain_label"] in domain_labels
for domain_label in domain_labels:
if pseudo_target["domain_label"] == domain_label:
domain = genome_camv.domains[domain_label]
target = Target(pseudo_target['label'],
pseudo_target['target_sequence'],
pseudo_target['target_sequence'],
pseudo_target['target_start_idx'],
pseudo_target['complex_concentration'],
pseudo_target['sense'],
domain)
domain.add_target(target)
""" isaac's testing block
target_P6_1 = Target("P6_1", "ggagaaagaaaagatatttaaaa", "ggagaaagaaaagatatttaaaa", 521, complex_concentration, 1, 1, gene_P6)
print P6_1.grna
print P6.target_location("P6_1")
print P6_1.cut_probability
P6_1.cut()
P6_1.repair(dt)
print P6_1.sequence
print P6.target_location("P6_1")
print P6_1.cut_probability
print P6_1.shift
"""
return genome_camv
def init_genome_camv(pseudo_targets):
""" Initializes the CaMV genome object for simulation
Args:
pseudo_targets: list of format [t1, t2, ..., tn]
where each is a dict with = {'label': ,
'target_sequence': ,
'target_start_idx': ,
'complex_concentration': ,
'sense': ,
'domain_label': }
Returns:
complete Genome instance corresponding to CaMV with targets
"""
# initialize camv genome
sequence = convert_fasta_to_string("genome_camv.fasta")
genome_camv = Genome(sequence)
# gene coordinates from http://www.ncbi.nlm.nih.gov/nuccore/9626938
# initialize camv genome
#untracked_small = Domain("untracked_small", 5674, 5775, "untracked", genome_camv) # removing for now, overlaps 19s
#genome_camv.add_domain(untracked_small)
#untracked_large = Domain("untracked_large", 7436, 8024, "untracked", genome_camv)
#genome_camv.add_domain(untracked_large)
untracked_large = Domain("untracked_large", 7436, 363, "untracked",
genome_camv)
genome_camv.add_domain(untracked_large)
promoter_35S = Domain("promoter_35S", 7092, 7435, "promoter", genome_camv)
genome_camv.add_domain(promoter_35S)
promoter_19S = Domain("promoter_19S", 5380, 5773, "promoter", genome_camv)
genome_camv.add_domain(promoter_19S)
gene_P1 = Domain("gene_P1",
364,
1347,
"orf",
genome_camv,
promoter=promoter_35S)
genome_camv.add_domain(gene_P1)
gene_P2 = Domain("gene_P2",
1349,
1828,
"orf",
genome_camv,
promoter=promoter_35S)
genome_camv.add_domain(gene_P2)
gene_P3 = Domain("gene_P3",
1830,
2219,
"orf",
genome_camv,
promoter=promoter_35S)
genome_camv.add_domain(gene_P3)
gene_P4 = Domain("gene_P4",
2201,
3670,
"orf",
genome_camv,
promoter=promoter_35S)
genome_camv.add_domain(gene_P4)
gene_P5 = Domain("gene_P5",
3633,
5672,
"orf",
genome_camv,
promoter=promoter_35S)
genome_camv.add_domain(gene_P5)
gene_P6 = Domain("gene_P6",
5776,
7338,
"orf",
genome_camv,
promoter=promoter_19S)
genome_camv.add_domain(gene_P6)
# initialize camv genome targets
domain_labels = genome_camv.domains.keys()
for pseudo_target in pseudo_targets:
assert pseudo_target["domain_label"] in domain_labels
for domain_label in domain_labels:
if pseudo_target["domain_label"] == domain_label:
domain = genome_camv.domains[domain_label]
target = Target(pseudo_target['label'],
pseudo_target['target_sequence'],
pseudo_target['target_sequence'],
pseudo_target['target_start_idx'],
pseudo_target['complex_concentration'],
pseudo_target['sense'], domain)
domain.add_target(target)
""" isaac's testing block
target_P6_1 = Target("P6_1", "ggagaaagaaaagatatttaaaa", "ggagaaagaaaagatatttaaaa", 521, complex_concentration, 1, 1, gene_P6)
print P6_1.grna
print P6.target_location("P6_1")
print P6_1.cut_probability
P6_1.cut()
P6_1.repair(dt)
print P6_1.sequence
print P6.target_location("P6_1")
print P6_1.cut_probability
print P6_1.shift
"""
return genome_camv