def open_fasta_file(self):
name = tkFileDialog.askopenfilename()
if name:
try:
self.f = Fasta(name)
self.loaded_file = os.path.split(name)[-1]
self.mlb.delete(0, self.mlb.size() - 1)
self.status.set("Loaded %s - %s" % (self.loaded_file, self.f))
self.scanmenu.entryconfig(0, state=NORMAL)
except:
tkMessageBox.showerror("Error opening file", "Error opening %s.\nIs it a valid FASTA file?" % os.path.split(name)[-1])
"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) +
