def scan_file(self):
d = ScanDialog(self.master)
if d.scan_ok:
min_spacer = d.min_spacer
max_spacer = d.max_spacer
nreport = d.nreport
cutoffs = []
if d.defaults:
cutoffs = DEFAULT_CUTOFFS
elif d.cutoff:
cutoffs = (max_spacer - min_spacer + 1) * [d.cutoff]
d.destroy()
self.status.set("Scanning %s for p53 binding sites" %
self.loaded_file)
self.mlb.delete(0, self.mlb.size() - 1)
count = 0
for (id, seq) in self.f.items():
result = scan(seq.upper(), PWM_LEFT, PWM_RIGHT, min_spacer,
max_spacer, cutoffs, nreport)
for (score, pos, spacer, strand) in result:
count += 1
self.mlb.insert(
END,
(id, pos, pos + len(PWM_LEFT) + spacer +
len(PWM_RIGHT), score, seq[pos:pos + len(PWM_LEFT)],
seq[pos + len(PWM_LEFT):pos + len(PWM_LEFT) + spacer],
seq[pos + len(PWM_LEFT) + spacer:pos + len(PWM_LEFT) +
spacer + len(PWM_RIGHT)]))
self.status.set("Done scanning %s. Found %s binding sites." %
(self.loaded_file, count))
self.filemenu.entryconfig(1, state=NORMAL)
def scan_file(self):
d = ScanDialog(self.master)
if d.scan_ok:
min_spacer = d.min_spacer
max_spacer = d.max_spacer
nreport = d.nreport
cutoffs = []
if d.defaults:
cutoffs = DEFAULT_CUTOFFS
elif d.cutoff:
cutoffs = (max_spacer - min_spacer + 1) * [d.cutoff]
d.destroy()
self.status.set("Scanning %s for p63 binding sites" % self.loaded_file)
self.mlb.delete(0, self.mlb.size() - 1)
count = 0
for (id,seq) in self.f.items():
result = scan(seq.upper(), PWM_LEFT, PWM_RIGHT, min_spacer, max_spacer, cutoffs, nreport)
for (score, pos, spacer, strand) in result:
count += 1
self.mlb.insert(END,(id, pos, pos + len(PWM_LEFT) + spacer + len(PWM_RIGHT), score,
seq[pos: pos + len(PWM_LEFT)],
seq[pos + len(PWM_LEFT): pos + len(PWM_LEFT) + spacer],
seq[pos + len(PWM_LEFT) + spacer: pos + len(PWM_LEFT) + spacer + len(PWM_RIGHT)]
))
self.status.set("Done scanning %s. Found %s binding sites." % (self.loaded_file, count))
self.filemenu.entryconfig(1, state=NORMAL)
s_max = max_score(pwm_left) + max_score(pwm_right)
s_min = min_score(pwm_left) + min_score(pwm_right)
sys.stderr.write(
"No cutoffs specified, using %s as a cutoff (%s of maxscore)\n" %
(SCORE_FRACTION * (s_max - s_min) + s_min, SCORE_FRACTION))
cutoffs = [
SCORE_FRACTION * (s_max - s_min) + s_min
for i in range(max_spacer - min_spacer + 1)
]
bed = options.bed
f = Fasta(inputfile)
for (id, seq) in f.items():
result = scan(seq.upper(), pwm_left, pwm_right, min_spacer, max_spacer,
cutoffs, nreport)
for (score, pos, spacer, strand) in result:
if bed:
first = id.split(" ")[0]
(chr, loc) = first.split(":")
if loc:
(start, end) = map(int, loc.split("-"))
print "%s\t%s\t%s\t%s" % (chr, start + pos,
start + pos + len(pwm_left) +
spacer + len(pwm_right), score)
else:
print "%s\t%s\t%s\t%s" % (id, pos, pos + len(pwm_left) +
spacer + len(pwm_right), score)
else:
print "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s %s %s" % (
id, "p53scan", "misc_feature", pos,
if options.pwmfile:
id, pwm_left,pwm_right = read_pwm_with_spacer(options.pwmfile)
sys.stderr.write("PWM-file supplied, left halfsite: %s, right halfsite: %s\n" % (len(pwm_left), len(pwm_right)))
if not options.cutoff:
s_max = max_score(pwm_left) + max_score(pwm_right)
s_min = min_score(pwm_left) + min_score(pwm_right)
sys.stderr.write("No cutoffs specified, using %s as a cutoff (%s of maxscore)\n" % (SCORE_FRACTION * (s_max - s_min) + s_min, SCORE_FRACTION))
cutoffs = [SCORE_FRACTION * (s_max - s_min) + s_min for i in range(max_spacer - min_spacer + 1)]
bed = options.bed
f = Fasta(inputfile)
for (id,seq) in f.items():
result = scan(seq.upper(), pwm_left, pwm_right, min_spacer, max_spacer, cutoffs, nreport)
for (score, pos, spacer, strand) in result:
if bed:
first = id.split(" ")[0]
(chr,loc) = first.split(":")
if loc:
(start, end) = map(int, loc.split("-"))
print "%s\t%s\t%s\t%s" % (chr, start + pos, start + pos + len(pwm_left) + spacer + len(pwm_right), score)
else:
print "%s\t%s\t%s\t%s" % (id, pos, pos + len(pwm_left) + spacer + len(pwm_right), score)
else:
print "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s %s %s" % (
id,
"p53scan",
"misc_feature",
pos, pos + len(pwm_left) + spacer + len(pwm_right),