def run_fimo(meme_dir: str, fimo_dir: str, record: Record, options: ConfigType,
verbose: bool) -> int:
"""Set paths, check existing files and run FIMO in parallel on each predicted motif"""
if not os.path.exists(fimo_dir):
os.makedirs(fimo_dir)
args = []
for plus_minus in os.listdir(meme_dir):
motif_file = os.path.join(meme_dir, plus_minus, "meme.html")
sites_file = os.path.join(meme_dir, plus_minus, "binding_sites.fasta")
output_file = os.path.join(fimo_dir, plus_minus, "fimo.txt")
output_dir = os.path.join(fimo_dir, plus_minus)
# input file and binding sites file present and size not zero --> should be fine to use
if (os.path.isfile(motif_file) and os.path.getsize(motif_file) > 0
and os.path.isfile(sites_file)
and os.path.getsize(sites_file) > 0):
# output file already present and size not zero --> do not run FIMO again on this one
if os.path.isfile(
output_file) and os.path.getsize(output_file) > 0:
pass
else:
args.append([
"fimo",
"-verbosity",
"1",
"-motif",
"1",
"-thresh",
"0.00006",
"-oc",
output_dir,
motif_file,
os.path.join(options.output_dir,
record.name + "_promoter_sequences.fasta"),
])
errors = parallel_execute(args, verbose=verbose)
return sum(errors)
def run_meme(meme_dir: str, _options: ConfigType, verbose: bool) -> int:
"""Set paths, check existing files and run MEME in parallel on each promoter set"""
args = []
for plus_minus in os.listdir(meme_dir):
input_file = os.path.join(meme_dir, plus_minus, "promoters.fasta")
output_file = os.path.join(meme_dir, plus_minus, "meme.xml")
# input file present and size not zero --> should be fine to use
if os.path.isfile(input_file) and os.path.getsize(input_file) > 0:
# output file already present and size not zero --> do not run MEME again on this one
if os.path.isfile(
output_file) and os.path.getsize(output_file) > 0:
pass
else:
args.append([
"meme",
input_file,
"-oc",
os.path.dirname(input_file),
"-dna",
"-nostatus",
"-mod",
"anr",
"-nmotifs",
"1",
"-minw",
"6",
"-maxw",
"12",
"-revcomp",
"-evt",
"1.0e+005",
])
errors = parallel_execute(args, verbose=verbose)
return sum(errors)
def test_timeout(self):
start = time.time()
with self.assertRaisesRegex(RuntimeError, ""):
subprocessing.parallel_execute([["sleep", "10"]] * 2, timeout=1)
elapsed = time.time() - start
assert elapsed < 1.5
def test_actually_parallel(self):
start = time.time()
subprocessing.parallel_execute([["sleep", "1"]] * 2)
elapsed = time.time() - start
assert elapsed < 1.5