def test_search_premade_batches(self):
"""Test search with pre-made batches CommOnly, NoComm, AllEnzymes."""
seq = Seq('ACCCGAATTCAAAACTGACTGATCGATCGTCGACTG', IUPACAmbiguousDNA())
search = AllEnzymes.search(seq)
self.assertEqual(search[MluCI], [6])
# Check if '/' operator works as 'search':
search = CommOnly / seq
self.assertEqual(search[MluCI], [6])
# Also in reverse order:
search = seq / NonComm
self.assertEqual(search[McrI], [28])
def test_search_premade_batches(self):
"""Test search with pre-made batches CommOnly, NoComm, AllEnzymes."""
seq = Seq('ACCCGAATTCAAAACTGACTGATCGATCGTCGACTG', IUPACAmbiguousDNA())
search = AllEnzymes.search(seq)
self.assertEqual(search[MluCI], [6])
# Check if '/' operator works as 'search':
search = CommOnly / seq
self.assertEqual(search[MluCI], [6])
# Also in reverse order:
search = seq / NonComm
self.assertEqual(search[McrI], [28])
def get_product_seq(self):
seq = self.template_seq
enzyme = AllEnzymes.get(self.enzyme_name)
sites = enzyme.search(seq)
site = -1 + one(
sites,
ValueError(
f"{self.enzyme_name!r} does not cut {self.template_tag!r}."),
ValueError(
f"{self.enzyme_name!r} cuts {self.template_tag!r} {len(sites)} times."
),
)
return seq[site:] + seq[:site]
os.makedirs(OUT_DIR, exist_ok=True)
DEL_COORDS = (args.DEL_START, args.DEL_END)
DEL_NAME = args.DEL_NAME
HR_LENGTH = args.HR_LENGTH
ENZYME = args.ENZYME
# Check input
try:
genome = SeqIO.read(GENOME, "fasta")
except (FileNotFoundError, ValueError):
raise SystemExit("\n\terror: could not read genome file\n")
if (not all([coord in range(1, len(genome)+1) for coord in DEL_COORDS])
or DEL_COORDS[0] >= DEL_COORDS[1]):
raise SystemExit("\n\terror: invalid deletion coordinates\n")
if ENZYME in AllEnzymes:
enzyme = AllEnzymes.get(ENZYME)
else:
raise SystemExit("\n\terror: restriction enzyme not found\t")
log = open(os.path.join(OUT_DIR, DEL_NAME + "_primer_design.txt"), "w")
# Define initial regions
del_region = Region(DEL_COORDS, genome)
margin1_coords = (del_region.s() - MARGIN_SIZE + INTERNAL_MARGIN,
del_region.s() + INTERNAL_MARGIN)
margin1 = Region(margin1_coords, genome)
margin2_coords = (del_region.e() - INTERNAL_MARGIN,
del_region.e() + MARGIN_SIZE - INTERNAL_MARGIN)
margin2 = Region(margin2_coords, genome)
log.write(
sep + "##### PRIMER DESIGN FOR DELETION '%s' %d - %d (%.1f kb) #####\n"