def test_avoid_matches_with_phage():
PHAGE_TAXID = "697289"
collection = GenomeCollection()
index = collection.get_taxid_bowtie_index_path(PHAGE_TAXID, version="1")
problem = DnaOptimizationProblem(
sequence=random_dna_sequence(30, seed=123),
constraints=[AvoidMatches(bowtie_index=index, match_length=10)],
logger=None,
)
all_breaches = problem.constraints_evaluations().all_locations()
assert len(all_breaches) == 5
problem.resolve_constraints()
assert problem.all_constraints_pass()
def test_get_bowtie_index(tmpdir):
collection = GenomeCollection(data_dir=str(tmpdir))
path = collection.get_taxid_bowtie_index_path(PHAGE_TAXID, version="2")
assert os.path.exists(path + '.1.bt2')
"""Example of use for AvoidBlastMatches.
In this example we create a 1000bp random sequence, then edit out every match
with E. coli that is 14bp or longer.
"""
from dnachisel import DnaOptimizationProblem, random_dna_sequence, AvoidMatches
from genome_collector import GenomeCollection
# THIS CREATES THE ECOLI BLAST DATABASE ON YOUR MACHINE IF NOT ALREADY HERE
collection = GenomeCollection()
ecoli_index = collection.get_taxid_bowtie_index_path(511145, version="1")
# DEFINE AND SOLVE THE PROBLEM
problem = DnaOptimizationProblem(
sequence=random_dna_sequence(500, seed=123),
constraints=[
AvoidMatches(bowtie_index=ecoli_index, match_length=15, mismatches=1)
],
)
print(
"Constraints validity before optimization\n",
problem.constraints_text_summary(),
)
print("\nNow resolving the problems\n")
problem.resolve_constraints(final_check=True)
