def scan(infile, motifs, cutoff, nreport=1, it=False):
# Get configuration defaults
config = MotifConfig()
# Cutoff for motif scanning, only used if a cutoff is not supplied
default_cutoff = config.get_default_params()['scan_cutoff']
# Number of CPUs to use
ncpus = config.get_default_params()['ncpus']
cutoffs = parse_cutoff(motifs, cutoff, default_cutoff)
total_result = {}
jobs = []
fa = Fasta(infile)
for motif in motifs:
for i in range(0, len(fa), CHUNK):
total_result[motif] = {}
jobs.append(pool.apply_async(
scan_fa_with_motif,
(fa[i:i + CHUNK],
motif,
cutoffs[motif.id],
nreport,
)))
motifkey = dict([(m.id, m) for m in motifs])
for job in jobs:
motif, result = job.get()
total_result[motifkey[motif.id]].update(result)
return total_result
def scan(infile, motifs, cutoff, nreport=1, it=False):
# Get configuration defaults
config = MotifConfig()
# Cutoff for motif scanning, only used if a cutoff is not supplied
default_cutoff = config.get_default_params()['scan_cutoff']
# Number of CPUs to use
ncpus = config.get_default_params()['ncpus']
cutoffs = parse_cutoff(motifs, cutoff, default_cutoff)
job_server = pp.Server(secret="beetrootsoup")
if job_server.get_ncpus() > ncpus:
job_server.set_ncpus(ncpus)
total_result = {}
jobs = []
fa = Fasta(infile)
for motif in motifs:
for i in range(0, len(fa), CHUNK):
total_result[motif] = {}
jobs.append(job_server.submit(
scan_fa_with_motif,
(fa[i:i + CHUNK],
motif,
cutoffs[motif.id],
nreport,
),
(),()))
motifkey = dict([(m.id, m) for m in motifs])
for job in jobs:
motif, result = job()
total_result[motifkey[motif.id]].update(result)
return total_result
def scan_it(infile, motifs, cutoff, nreport=1, rc=True):
# Get configuration defaults
config = MotifConfig()
# Cutoff for motif scanning, only used if a cutoff is not supplied
default_cutoff = config.get_default_params()['scan_cutoff']
# Number of CPUs to use
ncpus = config.get_default_params()['ncpus']
cutoffs = parse_cutoff(motifs, cutoff, default_cutoff)
jobs = []
fa = Fasta(infile)
motifkey = dict([(m.id, m) for m in motifs])
for motif in motifs:
for i in range(0, len(fa), CHUNK):
jobs.append(pool.apply_async(
scan_fa_with_motif,
(fa[i:i + CHUNK],
motif,
cutoffs[motif.id],
nreport,
rc,
)))
while len(jobs) > 10:
job = jobs.pop(0)
motif, result = job.get()
yield motifkey[motif.id], result
for job in jobs:
motif, result = job.get()
yield motifkey[motif.id], result
def parse_threshold_values(motif_file, cutoff):
motifs = read_motifs(motif_file)
d = parse_cutoff(motifs, cutoff)
threshold = {}
for m in motifs:
c = m.pwm_min_score() + (m.pwm_max_score() -
m.pwm_min_score()) * d[m.id]
threshold[m.id] = c
return threshold
def load_motifs(motif_file, cutoff=0.95):
motifs = read_motifs(open(motif_file))
d = parse_cutoff(motifs, cutoff)
cutoffs = []
for m in motifs:
c = m.pwm_min_score() + (m.pwm_max_score() - m.pwm_min_score()) * d[m.id]
cutoffs.append(c)
return zip(motifs, cutoffs)
def load_motifs(motif_file, cutoff=0.95):
motifs = read_motifs(open(motif_file))
d = parse_cutoff(motifs, cutoff)
cutoffs = []
for m in motifs:
c = m.pwm_min_score() + (m.pwm_max_score() -
m.pwm_min_score()) * d[m.id]
cutoffs.append(c)
return zip(motifs, cutoffs)
def scan_it(infile, motifs, cutoff, nreport=1, rc=True):
# Get configuration defaults
config = MotifConfig()
# Cutoff for motif scanning, only used if a cutoff is not supplied
default_cutoff = config.get_default_params()['scan_cutoff']
# Number of CPUs to use
ncpus = config.get_default_params()['ncpus']
cutoffs = parse_cutoff(motifs, cutoff, default_cutoff)
job_server = pp.Server(secret="beetrootsoup")
pp.SHOW_EXPECTED_EXCEPTIONS # True
if job_server.get_ncpus() > ncpus:
job_server.set_ncpus(ncpus)
jobs = []
fa = Fasta(infile)
motifkey = dict([(m.id, m) for m in motifs])
for motif in motifs:
for i in range(0, len(fa), CHUNK):
jobs.append(job_server.submit(
scan_fa_with_motif,
(fa[i:i + CHUNK],
motif,
cutoffs[motif.id],
nreport,
rc,
),
(),()))
while len(jobs) > 10:
job = jobs.pop(0)
motif, result = job()
yield motifkey[motif.id], result
for job in jobs:
motif, result = job()
yield motifkey[motif.id], result