def test_get_blast_database(tmpdir):
collection = GenomeCollection(data_dir=str(tmpdir))
taxid = PHAGE_TAXID
path = collection.datafile_path(taxid, data_type="blast_nucl")
assert not os.path.exists(path + ".nsq")
# Test nucleotide database
blast_db_path = collection.get_taxid_blastdb_path(taxid, db_type="nucl")
assert path == blast_db_path
file_size = os.stat(blast_db_path + ".nsq").st_size
assert 50_000 > file_size > 30_000
# Test protein database
blast_db_path = collection.get_taxid_blastdb_path(taxid, db_type="prot")
file_size = os.stat(blast_db_path + ".psq").st_size
assert 60_000 > file_size > 40_000
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()
In this example we create a 1000bp random sequence, then edit out every match
with E. coli that is 14bp or longer.
"""
import os
from genome_collector import GenomeCollection
from dnachisel import (
DnaOptimizationProblem,
random_dna_sequence,
AvoidBlastMatches,
)
# 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
)
],
# This is the basic example of the README to get you started.
from genome_collector import GenomeCollection
import subprocess
# GET A BLAST PATH
collection = GenomeCollection()
db_path = collection.get_taxid_blastdb_path(taxid=511145, db_type="nucl")
process = subprocess.run([
"blastn",
"-db",
db_path,
"-query",
"basic_example_queries.fa",
"-out",
"basic_example_results.txt",
],
stderr=subprocess.PIPE)
if process.returncode:
raise OSError("BLAST failed: %s" % process.stderr)
print("All good! see basic_example_results.txt for results.")