def make_restriction_part(part_length, left_overhang, right_overhang,
enzyme, forbidden_enzymes, assembly_enzyme='BsmBI'):
l_left = len(left_overhang)
l_right = len(right_overhang)
left_overhang_location = (0, l_left)
right_overhang_location = (l_left + part_length,
l_left + part_length + l_right)
center_location = (l_left, l_left + part_length)
core_sequence = (left_overhang + dc.random_dna_sequence(part_length)
+ right_overhang)
enforce_enzyme = dc.EnforcePatternOccurence(
enzyme=enzyme, location=center_location)
problem = dc.DnaOptimizationProblem(
sequence=core_sequence,
constraints=[
dc.AvoidChanges(left_overhang_location),
dc.AvoidChanges(right_overhang_location),
] + [enforce_enzyme] + [
dc.AvoidPattern(enzyme=enzyme_name)
for enzyme_name in forbidden_enzymes + [assembly_enzyme]
]
)
problem.resolve_constraints()
core_sequence = dc.sequence_to_biopython_record(problem.sequence)
for loc in [left_overhang_location, right_overhang_location]:
dc.annotate_record(core_sequence, loc, 'overhang')
site_location = enforce_enzyme.evaluate(problem).data['matches'][0]
dc.annotate_record(core_sequence, site_location.to_tuple(), enzyme)
assembly_site = Restriction.__dict__[assembly_enzyme].site
flank = dc.sequence_to_biopython_record(assembly_site + 'A')
dc.annotate_record(flank, label='flank')
return flank + core_sequence + flank.reverse_complement()
def test_circular_sequence_basic():
np.random.seed(123)
# Until the feature gets more battle-test, we're making sure it works
# across a range of sequences.
for i in range(4):
dna_sequence = (
"CTC"
+ dc.random_dna_sequence(100)
+ "CGTCTC"
+ dc.random_dna_sequence(100)
+ "CGT"
)
problem = dc.CircularDnaOptimizationProblem(
sequence=dna_sequence,
constraints=[
dc.AvoidPattern("BsmBI_site"),
dc.EnforceGCContent(
mini=0.4, maxi=0.6, location=(150, 250), window=50
),
dc.UniquifyAllKmers(k=9, location=(10, 100)),
],
logger=None,
)
assert not problem.all_constraints_pass()
problem.resolve_constraints()
assert problem.all_constraints_pass()
def test_circular_sequence_optimize_with_report(tmpdir):
"""Test that the custom function of CircularDnaOptimizationProblems works.
"""
np.random.seed(123)
# Until the feature gets more battle-test, we're making sure it works
# across a range of sequences.
dna_sequence = (
"CTC"
+ dc.random_dna_sequence(100)
+ "CGTCTC"
+ dc.random_dna_sequence(100)
+ "CGT"
)
problem = dc.CircularDnaOptimizationProblem(
sequence=dna_sequence,
constraints=[
dc.AvoidPattern("BsmBI_site"),
dc.EnforceGCContent(
mini=0.4, maxi=0.6, location=(150, 250), window=50
),
dc.UniquifyAllKmers(k=9, location=(10, 100)),
],
logger=None,
)
target = os.path.join(str(tmpdir), "circular_with_solution")
os.mkdir(target)
assert os.listdir(target) == []
assert not problem.all_constraints_pass()
success, message, data = problem.optimize_with_report(target)
assert problem.all_constraints_pass()
record = problem.to_record()
assert str(record.seq) != dna_sequence
def test_whole_sequence_change_objective_20_going_down():
np.random.seed(123)
problem = dc.DnaOptimizationProblem(
sequence=20*"AT",
constraints=[dc.AvoidPattern("ATA")],
objectives=[dc.EnforceChanges(amount=20)],
)
problem.mutations_per_iteration = 2
problem.resolve_constraints()
assert problem.number_of_edits() >= 24
problem.optimize()
assert problem.number_of_edits() == 20
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_insert_and_erase_pattern():
numpy.random.seed(123)
protein = dc.random_protein_sequence(100)
pattern = "ATGC"
# CREATE A SEQUENCE WITH 0 PATTERN OCCURENCES
sequence = dc.random_compatible_dna_sequence(
sequence_length=300,
constraints=[
dc.EnforceTranslation(translation=protein),
dc.AvoidPattern(pattern),
],
logger=None,
)
# NOW INCREASE PATTERN OCCURENCES FROM 0 TO 5
problem = dc.DnaOptimizationProblem(
sequence=sequence,
constraints=[
dc.EnforcePatternOccurence(pattern, occurences=5),
dc.EnforceTranslation(),
],
logger=None,
)
assert problem.constraints[0].evaluate(problem).score == -5
problem.resolve_constraints()
assert problem.all_constraints_pass()
sequence = problem.sequence
# NOW DECREASE THE NUMBER OF OCCURENCES FROM 5 TO 2
problem = dc.DnaOptimizationProblem(
sequence=sequence,
constraints=[
dc.EnforcePatternOccurence(pattern, occurences=2),
dc.EnforceTranslation(),
],
logger=None,
)
assert problem.constraints[0].evaluate(problem).score == -3
problem.resolve_constraints()
assert problem.all_constraints_pass()
def work(self):
data = self.data
figures = []
self.logger(message="Generating report...")
records = records_from_data_files(data.files)
constraints = [
dc.AvoidPattern("BsaI_site"),
dc.AvoidPattern("BsmBI_site"),
dc.AvoidPattern("BbsI_site"),
dc.AvoidPattern("SapI_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),
dc.EnforceGCContent(mini=0.1, maxi=0.9, window=100),
dc.UniquifyAllKmers(k=15),
]
dataframe = cr.constraints_breaches_dataframe(constraints, records)
spreadsheet_io = BytesIO()
dataframe.to_excel(spreadsheet_io)
records = cr.records_from_breaches_dataframe(dataframe, records)
zipped_records = flametree.file_tree("@memory")
if data.include_genbanks:
for record in records:
target = zipped_records._file("%s.gb" % record.id)
write_record(record, target)
pdf_io = BytesIO()
cr.breaches_records_to_pdf(records, pdf_io, logger=self.logger)
return {
"pdf_report": {
"data":
data_to_html_data(
pdf_io.getvalue(),
"pdf",
filename="manufacturability_report.pdf",
),
"name":
"manufacturability_report.pdf",
"mimetype":
"application/pdf",
},
"records": {
"data":
data_to_html_data(
zipped_records._close(),
"zip",
filename="manufacturability_annotated_records.zip",
),
"name":
"manufacturability_annotated_records.zip",
"mimetype":
"application/zip",
},
"spreadsheet": {
"data":
data_to_html_data(
spreadsheet_io.getvalue(),
"xlsx",
filename="manufacturability_report.xlsx",
),
"name":
"manufacturability_report.xlsx",
"mimetype":
"vnd.openxmlformats-officedocument.spreadsheetml.sheet",
},
}
problem:
- The sequence is designed to have a cross-origin BsmBI site that will need
to be removed, because the location-less specification ``AvoidPattern``
is interpreted as applying to the full circle.
- The specification ``EnforceGCContent`` is cross-origin since its location is
1500-2500, and the sequence is ~2000bp long.
"""
import dnachisel as dc
dna_sequence = "CTC%sCGTCTC%sCGT" % (
dc.random_dna_sequence(1000),
dc.random_dna_sequence(1000),
)
constraints = [
dc.AvoidPattern("BsmBI_site"),
dc.EnforceGCContent(mini=0.4, maxi=0.6, location=(1500, 2500), window=50),
dc.UniquifyAllKmers(k=9, location=(10, 1000)),
]
problem = dc.CircularDnaOptimizationProblem(
sequence=dna_sequence, constraints=constraints
)
print("BEFORE OPTIMIZATION:\n\n", problem.constraints_text_summary())
problem.resolve_constraints()
print("AFTER OPTIMIZATION:\n\n", problem.constraints_text_summary())
from copy import deepcopy
from collections import OrderedDict
import dnachisel as dc
import pandas
import seaborn as sns
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(
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")
regex = "(CCCTTT){3}C{3}" # optimal pattern for i-motif formation
query_seq = (
dnachisel.random_dna_sequence(length=50)
+ i_motif
+ dnachisel.random_dna_sequence(length=50)
)
print(query_seq)
seq = Bio.Seq.Seq(query_seq)
# Find first occurrence:
print(seq.find(i_motif))
# Find all:
matches = [
(m.start(), m.end()) for m in re.finditer(i_motif, str(seq))
] # list of tuples
print(seq[matches[0][0] : matches[0][1]])
# Find regex with DNA Chisel:
problem = dnachisel.DnaOptimizationProblem(
sequence=query_seq, constraints=[dnachisel.AvoidPattern(pattern=regex)]
)
print(problem.constraints_text_summary())
compact_regex = "(C{3}T{3}){3}C{3}" # variant of the same regex
problem = dnachisel.DnaOptimizationProblem(
sequence=query_seq, constraints=[dnachisel.AvoidPattern(pattern=compact_regex)]
)
print(problem.constraints_text_summary())