def test_constraints_reports():
genbank_dir = os.path.join("tests", "data", "10_emma_genbanks")
records = [
dc.load_record(os.path.join(genbank_dir, filename), name=filename)
for filename in os.listdir(genbank_dir)
]
# DEFINE THE CONSTRAINTS TO BE CHECKED ON EACH RECORD
constraints = [
dc.AvoidPattern("BsaI_site"),
dc.AvoidPattern("BsmBI_site"),
dc.AvoidPattern("BbsI_site"),
dc.AvoidPattern("8x1mer"),
dc.AvoidPattern("5x3mer"),
dc.AvoidPattern("9x2mer"),
dc.AvoidHairpins(stem_size=20, hairpin_window=200),
dc.EnforceGCContent(mini=0.3, maxi=0.7, window=100),
]
# CREATE A SPREADSHEET AND PLOTS OF THE BREACHES
dataframe = cr.constraints_breaches_dataframe(constraints, records)
records = cr.records_from_breaches_dataframe(dataframe, records)
assert sum([len(r.features) for r in records]) == 157
pdf_data = cr.breaches_records_to_pdf(records)
assert 70000 < len(pdf_data) < 72000
def test_optimization_2():
sequence_path = os.path.join("tests", "data",
"test_optimization_sequence_2.fa")
sequence = str(load_record(sequence_path).seq)[:5500]
deluxe_dna = CommercialDnaOffer(
name="DeluxeDNA.com",
sequence_constraints=[SequenceLengthConstraint(max_length=4000)],
pricing=PerBasepairPricing(0.20),
lead_time=10,
)
cheap_dna = CommercialDnaOffer(
name="CheapDNA.com",
sequence_constraints=[
NoPatternConstraint(enzyme="BsaI"),
EnforceGCContent(0.3, 0.7, window=60),
],
pricing=PerBasepairPricing(0.10),
lead_time=15,
)
# BLOCKS TO CHUNKS ASSEMBLY
gibson_blocks_assembly_station = DnaAssemblyStation(
name="Gibson Blocks Assembly",
assembly_method=GibsonAssemblyMethod(
overhang_selector=FixedSizeSegmentSelector(10),
min_segment_length=1000,
max_segment_length=6000,
duration=8,
cost=16,
),
supplier=[deluxe_dna, cheap_dna],
coarse_grain=30,
fine_grain=False,
memoize=True,
# a_star_factor="auto",
)
quote_before = gibson_blocks_assembly_station.get_quote(sequence)
assert quote_before.price > 850
objective = OptimizeManufacturability(gibson_blocks_assembly_station)
problem = DnaOptimizationProblem(
sequence=sequence,
constraints=[EnforceTranslation(location=(0, 4998))],
objectives=[objective],
)
problem.randomization_threshold = 0 # Forces "random search" mode
problem.max_random_iters = 5
problem.optimize()
print("OPTIMIZATION DONE, GENERATING REPORT")
quote_after = gibson_blocks_assembly_station.get_quote(problem.sequence)
assert quote_after.price < 580
def test_cuba_example_1():
path = os.path.join('tests', 'tests_from_genbanks', 'genbanks',
'cuba_example_1.gbk')
record = load_record(path)
problem = DnaOptimizationProblem.from_record(record)
assert not problem.all_constraints_pass()
problem.resolve_constraints()
assert problem.all_constraints_pass()
assert problem.objective_scores_sum() < -100
problem.optimize()
assert problem.objective_scores_sum() > -0.1
def test_optimization_1():
company_ingen = CommercialDnaOffer(
name="Company InGen",
pricing=PerBasepairPricing(0.08),
sequence_constraints=[NoPatternConstraint(enzyme="AarI")],
)
company_delux = CommercialDnaOffer(
name="Company Delux",
pricing=PerBasepairPricing(0.66),
sequence_constraints=[],
)
assembly_station = DnaAssemblyStation(
name="Gibson Assembly Station",
assembly_method=GibsonAssemblyMethod(
overhang_selector=FixedSizeSegmentSelector(20),
min_segment_length=200,
max_segment_length=1200,
),
supplier=[company_ingen, company_delux],
coarse_grain=20,
# a_star_factor="auto",
)
sequence_path = os.path.join("tests", "data",
"test_optimization_sequence_1.fa")
sequence = load_record(sequence_path)
objective = OptimizeManufacturability(assembly_station)
problem = DnaOptimizationProblem(sequence=sequence, objectives=[objective])
quote = objective.get_quote(problem)
score = problem.objective_scores_sum()
assert -367 < score < -366
problem.randomization_threshold = 0
problem.max_random_iters = 5
problem.optimize()
score = problem.objective_scores_sum()
assert -244 < score < -243
DnaOptimizationProblem,
load_record,
Location,
EnforceTranslation,
EnforceGCContent,
AvoidPattern,
)
print("DOWNLOADING AND PARSING THE GENBANK DATA...")
url = (
"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
+ "db=nucleotide&id=48994873&rettype=gb&retmode=txt"
)
genbank_data = request.urlopen(url).read().decode("utf-8")
genbank_record = load_record(StringIO(genbank_data), file_format="genbank")
print("INITIALIZING THE PROBLEM WITH CONSTRAINTS FOR EACH GENE...")
constraints = []
for feature in genbank_record.features:
if feature.type == "gene" and len(feature.location.parts) == 1:
location = Location.from_biopython_location(feature.location)
if (len(location) % 3 == 0) and len(location) > 100:
gene_constraints = [
EnforceTranslation(location = location),
AvoidPattern("BsmBI_site", location),
EnforceGCContent(
mini=0.40, maxi=0.60, window=150, location=location
),
]
"""Example of use of the AvoidChanges as an objective to minimize modifications
of a sequence."""
import os
from dnachisel import (AvoidBlastMatches, random_dna_sequence,
DnaOptimizationProblem, load_record)
sequence_path = os.path.join("tests", "data", "example_sequence.gbk")
sequence = str(load_record(sequence_path).seq.upper())
def test_avoid_blast_matches():
avoided_seqs = [
"GTCCTCATGCGAAAGCTACGATCGCCAACCCTGT",
"ACCCACCTCGTTACGTCCACGGCACGAGGAATGATCTCGAGTTGCTTT"
]
constraint = AvoidBlastMatches(sequences=avoided_seqs, min_align_length=8)
problem = DnaOptimizationProblem(sequence=sequence,
constraints=[constraint])
assert not problem.all_constraints_pass()
cst_eval = constraint.evaluate(problem)
assert len(cst_eval.locations) == 10
problem.resolve_constraints()
assert problem.all_constraints_pass()
sns.set()
# DEFINE HOW OPTIMIZATION PROBLEMS ARE CREATED
specifications = {
"~keep": dc.AvoidChanges(),
"~no(CG)": dc.AvoidPattern("CG"),
"~codon_optimize": dc.CodonOptimize(species="e_coli"),
"~unique_kmers": dc.UniquifyAllKmers(20),
"~gc(39%)": dc.EnforceGCContent(target=0.39, window=200),
}
class_to_label = {
spec.__class__: label for label, spec in specifications.items()
}
sequence = dc.load_record("record.gb")
def create_problem(boost_profile):
location = dc.Location(1000, 9247)
objectives = []
for spec_name, boost in boost_profile.items():
spec = specifications[spec_name]
spec = spec.copy_with_changes(boost=boost, location=location)
objectives.append(spec)
return dc.DnaOptimizationProblem(
sequence,
constraints=[dc.EnforceTranslation(location=location)],
objectives=objectives,
)
AvoidPattern,
AvoidChanges,
EnforceTranslation,
HomopolymerPattern,
EnforceGCContent,
CodonOptimize,
load_record,
)
from io import StringIO
import urllib
# DOWNLOAD THE PLASMID FROM THE WEB (it is a 7kb plasmid with 3 genes)
url = "http://www.stevekellylab.com/constructs/pDex/pDex577-G.gb"
response = urllib.request.urlopen(url)
record_file = StringIO(response.read().decode("utf-8"))
record = load_record(record_file, fmt="genbank")
CDS_list = [(int(f.location.start), int(f.location.end),
int(f.location.strand)) for f in record.features
if f.type == "CDS"]
# DEFINE CONSTRAINTS
dna_provider_constraints = [
AvoidPattern("BsaI_site"),
AvoidPattern("AarI_site"),
AvoidPattern("9xA"),
AvoidPattern("9xT"),
AvoidPattern(HomopolymerPattern("6xG")),
AvoidPattern(HomopolymerPattern("6xC")),
EnforceGCContent(0.4, 0.65),
def test_genbank_import_from_record_unknown_specs():
record = load_record(example_sequence_path)
with pytest.raises(TypeError):
_ = DnaOptimizationProblem.from_record(
record, specifications_dict={}
)
def test_genbank_import_from_record():
record = load_record(example_sequence_path)
problem = DnaOptimizationProblem.from_record(record)
assert len(problem.constraints) == 5
assert len(problem.objectives) == 3
from urllib import request
from io import StringIO
from dnachisel import (DnaOptimizationProblem, load_record, Location,
EnforceTranslation, EnforceGCContent, AvoidPattern)
print("DOWNLOADING AND PARSING THE GENBANK DATA...")
url="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?" + \
"db=nucleotide&id=48994873&rettype=gb&retmode=txt"
genbank_data = request.urlopen(url).read().decode('utf-8')
genbank_record = load_record(StringIO(genbank_data), fmt="genbank")
print("INITIALIZING THE PROBLEM WITH CONSTRAINTS FOR EACH GENE...")
constraints = []
for feature in genbank_record.features:
if feature.type == 'gene' and len(feature.location.parts) == 1:
location = Location.from_biopython_location(feature.location)
if (len(location) % 3 == 0) and len(location) > 100:
constraints.extend([
EnforceTranslation(location),
AvoidPattern('BsmBI_site', location),
EnforceGCContent(mini=0.40,
maxi=0.60,
window=150,
location=location)
])
problem = DnaOptimizationProblem(genbank_record, constraints)
print("RESOLVING THE CONSTRAINTS...")
import dnachisel as dc
import dnachisel.reports.constraints_reports as cr
import os
# IMPORT THE 10 RECORDS FROM THE genbanks/ FOLDER
records = [
dc.load_record(os.path.join("genbanks", filename), name=filename)
for filename in os.listdir("genbanks")
]
# DEFINE THE CONSTRAINTS TO BE CHECKED ON EACH RECORD
constraints = [
dc.AvoidPattern("BsaI_site"),
dc.AvoidPattern("BsmBI_site"),
dc.AvoidPattern("BbsI_site"),
dc.AvoidPattern("8x1mer"),
dc.AvoidPattern("5x3mer"),
dc.AvoidPattern("9x2mer"),
dc.AvoidHairpins(stem_size=20, hairpin_window=200),
dc.EnforceGCContent(mini=0.3, maxi=0.7, window=100),
]
# CREATE A SPREADSHEET AND PLOTS OF THE BREACHES
dataframe = cr.constraints_breaches_dataframe(constraints, records)
dataframe.to_excel("breaches.xlsx")
records = cr.records_from_breaches_dataframe(dataframe, records)
cr.breaches_records_to_pdf(records, "breaches_plots.pdf")
much improved.
The final sequence (with the original annotations) is exported to Genbank.
"""
from dnachisel import (DnaOptimizationProblem, AvoidPattern, AvoidChanges,
EnforceTranslation, HomopolymerPattern,
EnforceGCContent, CodonOptimize, load_record)
from io import StringIO
import urllib
# DOWNLOAD THE PLASMID FROM THE WEB (it is a 7kb plasmid with 3 genes)
url = "http://www.stevekellylab.com/constructs/pDex/pDex577-G.gb"
response = urllib.request.urlopen(url)
record_file = StringIO(response.read().decode('utf-8'))
record = load_record(record_file, fmt='genbank')
CDS_list = [(int(f.location.start), int(f.location.end),
int(f.location.strand)) for f in record.features
if f.type == "CDS"]
# DEFINE CONSTRAINTS
dna_provider_constraints = [
AvoidPattern("BsaI_site"),
AvoidPattern("AarI_site"),
AvoidPattern(HomopolymerPattern("A", 9)),
AvoidPattern(HomopolymerPattern("T", 9)),
AvoidPattern(HomopolymerPattern("G", 6)),
AvoidPattern(HomopolymerPattern("C", 9)),
EnforceGCContent(0.4, 0.65),
