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()
def test_avoid_phage_blast_matches():
PHAGE_TAXID = "697289"
collection = GenomeCollection()
blastdb = collection.get_taxid_blastdb_path(PHAGE_TAXID, db_type="nucl")
problem = DnaOptimizationProblem(sequence=random_dna_sequence(30,
seed=123),
constraints=[
AvoidBlastMatches(blast_db=blastdb,
min_align_length=10,
word_size=7)
],
logger=None)
assert not problem.all_constraints_pass()
problem.resolve_constraints()
assert problem.all_constraints_pass()
if not os.path.exists('downloaded_data'):
os.mkdir('downloaded_data')
if not os.path.exists(os.path.join('downloaded_data', 'ecoli_genome.nsq')):
urlretrieve(ecoli_genome_url, genome_gz)
with open(genome_fasta, 'wb') as f_fasta:
with gzip.open(genome_gz, 'rb') as f_gz:
shutil.copyfileobj(f_gz, f_fasta)
subprocess.Popen([
"makeblastdb", "-in", genome_fasta, "-dbtype", "nucl", "-out",
genome_blastdb
])
# DEFINE AND SOLVE THE PROBLEM
problem = DnaOptimizationProblem(sequence=random_dna_sequence(1000, seed=123),
constraints=[
AvoidBlastMatches(blast_db=genome_blastdb,
min_align_length=13,
perc_identity=95)
])
print("\nConstraints validity before optimization\n")
print(problem.constraints_text_summary())
print("\nLet's resolve these problems:\n")
problem.resolve_constraints()
print("\nAfter optimization\n")
print(problem.constraints_text_summary())
from dnachisel import (
DnaOptimizationProblem,
random_dna_sequence,
AvoidBlastMatches,
)
# THIS CREATES THE ECOLI BLAST DATABASE ON YOUR MACHINE IF NOT ALREADY HERE
download_ecoli_genome_if_not_already_there()
# DEFINE AND SOLVE THE PROBLEM
problem = DnaOptimizationProblem(
sequence=random_dna_sequence(1000, seed=123),
constraints=[
AvoidBlastMatches(
blast_db=os.path.join("downloaded_data", "ecoli_genome"),
min_align_length=13,
perc_identity=95,
)
],
)
print("\n\nWarning! BLASTing can take a long time! Be patient.", end="\n\n")
print(
"Constraints validity before optimization\n",
problem.constraints_text_summary(),
)
print("\nLet's resolve these problems:\n")
problem.resolve_constraints()
print("\nAfter optimization\n")
print(problem.constraints_text_summary())
)
# THIS CREATES THE ECOLI BLAST DATABASE ON YOUR MACHINE IF NOT ALREADY HERE
collection = GenomeCollection()
ecoli_blastdb = collection.get_taxid_blastdb_path(511145, db_type="nucl")
# DEFINE AND SOLVE THE PROBLEM
problem = DnaOptimizationProblem(
sequence=random_dna_sequence(500, seed=123),
constraints=[
AvoidBlastMatches(
blast_db=ecoli_blastdb,
min_align_length=13,
perc_identity=100,
word_size=5, # The bigger the word size, the faster
e_value=1e20,
# ungapped=False
)
],
)
print(
"Constraints validity before optimization\n",
problem.constraints_text_summary(),
)
print("\nNow resolving the problems\n")
problem.resolve_constraints(final_check=True)
print(