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])
max_spacer = int(options.spacer)
if options.cutoff:
cutoff = options.cutoff
if options.pwmfile:
id, pwm_left,pwm_middle,pwm_right = read_pwm_triplet(options.pwmfile)
sys.stderr.write("PWM-file supplied, left site: %s, middle site: %s, right site: %s\n" % (len(pwm_left), len(pwm_middle), len(pwm_right)))
if not options.cutoff:
s_max = max_score(pwm_left) + max_score(pwm_right) + max_score(pwm_middle)
s_min = min_score(pwm_left) + min_score(pwm_right) + min_score(pwm_middle)
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))
cutoff = SCORE_FRACTION * (s_max - s_min) + s_min
bed = options.bed
f = Fasta(inputfile)
for (id,seq) in f.items():
result = scan_triplet(seq.upper(), pwm_left, pwm_middle, pwm_right, min_spacer, max_spacer, cutoff, nreport)
for (score, pos, spacer1, spacer2, 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) + spacer1 + len(pwm_middle) + spacer2 + len(pwm_right), score)
else:
print "%s\t%s\t%s\t%s" % (id, pos, pos + len(pwm_left) + spacer1 + len(pwm_middle) + spacer2 + 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 %s %s" % (
id,
"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) +
class App:
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])
def save_results(self):
name = tkFileDialog.asksaveasfilename(filetypes=[("gff", "*.gff")],
defaultextension=".gff")
if name:
f = open(name, "w")
for row in self.mlb.get(0, self.mlb.size() - 1):
f.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s %s %s\n" %
(row[0], "p53scan", "p53bs", row[1], row[2], row[3],
"+", ".", row[4], row[5], row[6]))
f.close()
self.status.set("p53scan results written to %s" %
os.path.split(name)[-1])
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 exit(self):
sys.exit()
def resize(self, event):
frame.pack()
def about(self):
tkMessageBox.showinfo("About %s" % NAME, DESCRIPTION)
def __init__(self, master):
# create a menu
self.master = master
master.title("p53scan")
menu = Menu(master)
master.config(menu=menu)
self.filemenu = Menu(menu, tearoff=0)
menu.add_cascade(label="File", menu=self.filemenu)
self.filemenu.add_command(label="Open Fastafile...",
command=self.open_fasta_file)
self.filemenu.add_command(label="Save Results...",
command=self.save_results)
self.filemenu.add_separator()
self.filemenu.add_command(label="Exit", command=self.exit)
self.filemenu.entryconfig(1, state=DISABLED)
self.scanmenu = Menu(menu, tearoff=0)
menu.add_cascade(label="Scan", menu=self.scanmenu)
self.scanmenu.add_command(label="Scan file", command=self.scan_file)
self.scanmenu.entryconfig(1, state=DISABLED)
helpmenu = Menu(menu, tearoff=0)
menu.add_cascade(label="Help", menu=helpmenu)
helpmenu.add_command(label="About...", command=self.about)
self.status = StatusBar(master)
self.status.pack(side=BOTTOM, fill=X)
self.status.set("No file loaded")
self.mlb = MultiListbox(master, (('id', 30), ('start', 4), ('end', 4),
('score', 4), ('left', 15),
('spacer', 10), ('right', 15)))
self.mlb.pack(expand=YES, fill=BOTH)
class App:
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])
def save_results(self):
name = tkFileDialog.asksaveasfilename(filetypes=[("gff", "*.gff")], defaultextension=".gff")
if name:
f = open(name, "w")
for row in self.mlb.get(0, self.mlb.size() - 1):
f.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s %s %s\n" % (row[0], "p63scan", "p63bs", row[1], row[2], row[3], "+", ".", row[4], row[5], row[6]))
f.close()
self.status.set("p63scan results written to %s" % os.path.split(name)[-1])
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)
def exit(self):
sys.exit()
def resize(self, event):
frame.pack()
def about(self):
tkMessageBox.showinfo("About %s" % NAME, DESCRIPTION)
def __init__(self, master):
# create a menu
self.master = master
master.title("p63scan")
menu = Menu(master)
master.config(menu=menu)
self.filemenu = Menu(menu,tearoff=0)
menu.add_cascade(label="File", menu=self.filemenu)
self.filemenu.add_command(label="Open Fastafile...", command=self.open_fasta_file)
self.filemenu.add_command(label="Save Results...", command=self.save_results)
self.filemenu.add_separator()
self.filemenu.add_command(label="Exit", command=self.exit)
self.filemenu.entryconfig(1, state=DISABLED)
self.scanmenu = Menu(menu,tearoff=0)
menu.add_cascade(label="Scan", menu=self.scanmenu)
self.scanmenu.add_command(label="Scan file", command=self.scan_file)
self.scanmenu.entryconfig(1, state=DISABLED)
helpmenu = Menu(menu,tearoff=0)
menu.add_cascade(label="Help", menu=helpmenu)
helpmenu.add_command(label="About...", command=self.about)
self.status = StatusBar(master)
self.status.pack(side=BOTTOM, fill=X)
self.status.set("No file loaded")
self.mlb = MultiListbox(master, (('id', 30), ('start', 4),('end',4), ('score', 4), ('left', 15), ('spacer', 10), ('right', 15)))
self.mlb.pack(expand=YES, fill=BOTH)
