def maxenr(args):
if not os.path.exists(args.sample):
print "File %s does not exist!" % args.sample
exit(1)
if not os.path.exists(args.background):
print "File %s does not exist!" % args.background
exit(1)
pwmfile = args.pwmfile
fg_file = args.sample
bg_file = args.background
motifs = dict([(x.id, x) for x in pwmfile_to_motifs(pwmfile)])
ids = []
if args.ids:
ids = args.ids.split(",")
else:
ids = motifs.keys()
fg_jobs = {}
bg_jobs = {}
for id in ids:
if motifs.has_key(id):
bg_jobs[id] = pool.apply_async(get_scores, (motifs[id], bg_file))
fg_jobs[id] = pool.apply_async(get_scores, (motifs[id], fg_file))
else:
print "Wrong id: %s" % id
sys.exit()
print "Motif\t# matches\tMax. enrichment\tScore\tCutoff"
for id in ids:
pos = array(fg_jobs[id].get())
neg = array(bg_jobs[id].get())
factor = len(neg) / float(len(pos))
scores = array([s for s in hstack((pos, neg)) if sum(neg >= s) > 1])
enr = array([(sum(pos >= x) / float(sum(neg >= x))) * factor for x in scores])
# print len(scores), len(enr)
# for x,y in zip(enr, scores):
# print "%s\t%s" % (x,y)
max_score = scores[enr.argmax()]
cutoff = (max_score - motifs[id].pwm_min_score()) / (motifs[id].pwm_max_score() - motifs[id].pwm_min_score())
print "%s\t%s\t%0.2f\t%0.2f\t%0.3f" % (
id,
sum(pos >= scores[enr.argmax()]),
max(enr),
scores[enr.argmax()],
cutoff,
)
def location(args):
fastafile = args.fastafile
pwmfile = args.pwmfile
lwidth = args.width
if not lwidth:
f = Fasta(fastafile)
lwidth = len(f.items()[0][1])
f = None
jobs = []
motifs = pwmfile_to_motifs(pwmfile)
ids = [motif.id for motif in motifs]
if args.ids:
ids = args.ids.split(",")
for motif in motifs:
if motif.id in ids:
outfile = os.path.join("%s_histogram" % motif.id)
jobs.append(
pool.apply_async(
motif_localization,
(fastafile,motif,lwidth,outfile, args.cutoff)
))
for job in jobs:
job.get()
def location(args):
"""
Creates histrogram of motif location.
Parameters
----------
args : argparse object
Command line arguments.
"""
fastafile = args.fastafile
pwmfile = args.pwmfile
lwidth = args.width
if not lwidth:
f = Fasta(fastafile)
lwidth = len(f.items()[0][1])
f = None
jobs = []
motifs = pwmfile_to_motifs(pwmfile)
ids = [motif.id for motif in motifs]
if args.ids:
ids = args.ids.split(",")
for motif in motifs:
if motif.id in ids:
outfile = os.path.join("%s_histogram" % motif.id)
jobs.append(
pool.apply_async(
motif_localization,
(fastafile, motif, lwidth, outfile, args.cutoff)))
for job in jobs:
job.get()
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_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 maxenr(args):
if not os.path.exists(args.sample):
print "File %s does not exist!" % args.sample
exit(1)
if not os.path.exists(args.background):
print "File %s does not exist!" % args.background
exit(1)
pwmfile = args.pwmfile
fg_file = args.sample
bg_file = args.background
motifs = dict([(x.id, x) for x in pwmfile_to_motifs(pwmfile)])
ids = []
if args.ids:
ids = args.ids.split(",")
else:
ids = motifs.keys()
fg_jobs = {}
bg_jobs = {}
for id in ids:
if motifs.has_key(id):
bg_jobs[id] = pool.apply_async(get_scores, (
motifs[id],
bg_file,
))
fg_jobs[id] = pool.apply_async(get_scores, (
motifs[id],
fg_file,
))
else:
print "Wrong id: %s" % id
sys.exit()
print "Motif\t# matches\tMax. enrichment\tScore\tCutoff"
for id in ids:
pos = array(fg_jobs[id].get())
neg = array(bg_jobs[id].get())
factor = len(neg) / float(len(pos))
scores = array([s for s in hstack((pos, neg)) if sum(neg >= s) > 1])
enr = array([(sum(pos >= x) / float(sum(neg >= x))) * factor
for x in scores])
#print len(scores), len(enr)
#for x,y in zip(enr, scores):
# print "%s\t%s" % (x,y)
max_score = scores[enr.argmax()]
cutoff = (max_score - motifs[id].pwm_min_score()) / (
motifs[id].pwm_max_score() - motifs[id].pwm_min_score())
print "%s\t%s\t%0.2f\t%0.2f\t%0.3f" % (
id, sum(pos >= scores[enr.argmax()]), max(enr),
scores[enr.argmax()], cutoff)
