def export(self):
"""Export selected text to new text window."""
seq = self.get_selection_or_sequence()
if not seq:
return
np = NotePad()
tid = np.text_id()
tid.insert('end', seq)
def export(self):
"""Export selected text to new text window."""
seq = self.get_selection_or_sequence()
if not seq:
return
np = NotePad()
tid = np.text_id()
tid.insert('end', seq)
def gcframe(self, direction='both'):
seq = self.get_selection_or_sequence()
if not seq:
return
np = NotePad()
tid = np.text_id()
tid.insert('end',
self.translator.gcframe(seq, self.current_codon_table_id,
direction))
def translate(self):
seq = self.get_selection_or_sequence()
frame = self.frame_int.get()
if not seq:
return
np = NotePad()
tid = np.text_id()
tid.insert('end',
self.translator.frame_nice(seq, frame,
self.current_codon_table_id))
def extract(self):
seq = self.get_selection_or_sequence()
frame = self.frame_int.get()
if not seq:
return
aa_seq = self.translator.frame(seq, frame, self.current_codon_table_id)
aa_seq = re.sub('(.{50})', '\\1\n', str(aa_seq))
np = NotePad()
tid = np.text_id()
tid.insert('end', '>frame%d\n%s' % (frame, aa_seq))
def gcframe(self, direction='both'):
seq = self.get_selection_or_sequence()
if not seq:
return
np = NotePad()
tid = np.text_id()
tid.insert(
'end',
self.translator.gcframe(seq, self.current_codon_table_id,
direction))
def gcframe(self, direction="both"):
"""Run pretty print multiple frame translations."""
seq = self.get_selection_or_sequence()
if not seq:
return
np = NotePad()
tid = np.text_id()
tid.insert(
"end", self.translator.gcframe(seq, self.current_codon_table_id, direction)
)
def extract(self):
seq = self.get_selection_or_sequence()
frame = self.frame_int.get()
if not seq:
return
aa_seq = self.translator.frame(seq, frame, self.current_codon_table_id)
aa_seq = re.sub('(.{50})', '\\1\n', str(aa_seq))
np = NotePad()
tid = np.text_id()
tid.insert('end', '>frame%d\n%s' % (frame, aa_seq))
def translate(self):
seq = self.get_selection_or_sequence()
frame = self.frame_int.get()
if not seq:
return
np = NotePad()
tid = np.text_id()
tid.insert(
'end',
self.translator.frame_nice(seq, frame,
self.current_codon_table_id))
def extract(self):
"""Make single frame translation and display aa sequence as fasta."""
seq = self.get_selection_or_sequence()
frame = self.frame_int.get()
if not seq:
return
aa_seq = self.translator.frame(seq, frame, self.current_codon_table_id)
aa_seq = re.sub("(.{50})", "\\1\n", str(aa_seq))
np = NotePad()
tid = np.text_id()
tid.insert("end", ">frame%d\n%s" % (frame, aa_seq))
def translate(self):
"""Run pretty print single frame translation."""
seq = self.get_selection_or_sequence()
frame = self.frame_int.get()
if not seq:
return
np = NotePad()
tid = np.text_id()
tid.insert(
"end", self.translator.frame_nice(seq, frame, self.current_codon_table_id)
)
def Run(self):
self.notepad = NotePad()
tid = self.notepad.tid
self.notepad.menubar.configure(bg='red')
self.toplevel.destroy()
blastbg = xbb_blastbg.BlastDisplayer(self.command, tid)
blastbg.RunCommand()
# indicate the finished run by changing color
try:
self.notepad.menubar.configure(bg='green4')
except:
pass
def Run(self):
self.notepad = NotePad()
tid = self.notepad.tid
self.toplevel.destroy()
blastbg = xbb_blastbg.BlastDisplayer(self.command_data, tid)
blastbg.RunCommand()
def Run(self):
"""Open new notepad and initialize running BLAST."""
self.notepad = NotePad()
tid = self.notepad.tid
self.toplevel.destroy()
blastbg = xbb_blastbg.BlastDisplayer(self.command_data, tid)
blastbg.RunCommand()
def statistics(self):
seq = self.get_selection_or_sequence()
if not seq:
return
seq = seq.upper()
aa = {'A': 0, 'C': 0, 'G': 0, 'T': 0, 'N': 0}
for nt in seq:
if nt not in aa:
nt = 'N'
aa[nt] = aa[nt] + 1
GC = (100.0 * (aa['G'] + aa['C'])) / len(seq)
np = NotePad()
tid = np.text_id()
tid.insert('end', "%s\n\n" %
(time.strftime('%y %b %d, %X\n',
time.localtime(time.time()))) +
"Length = %d\nA=%d C=%d G=%d T=%d other=%d\nGC=%f\n\n" %
(len(seq), aa['A'], aa['C'], aa['G'], aa['T'], aa['N'], GC))
def statistics(self):
seq = self.get_selection_or_sequence()
if not seq:
return
seq = seq.upper()
aa = {'A': 0, 'C': 0, 'G': 0, 'T': 0, 'N': 0}
for nt in seq:
if nt not in aa:
nt = 'N'
aa[nt] = aa[nt] + 1
GC = (100.0 * (aa['G'] + aa['C'])) / len(seq)
np = NotePad()
tid = np.text_id()
tid.insert(
'end', "%s\n\n" %
(time.strftime('%y %b %d, %X\n', time.localtime(time.time()))) +
"Length = %d\nA=%d C=%d G=%d T=%d other=%d\nGC=%f\n\n" %
(len(seq), aa['A'], aa['C'], aa['G'], aa['T'], aa['N'], GC))
def statistics(self):
"""Calculate statistics of sequence and display in new window."""
seq = self.get_selection_or_sequence()
if not seq:
return
seq = seq.upper()
aa = {"A": 0, "C": 0, "G": 0, "T": 0, "N": 0}
for nt in seq:
if nt not in aa:
nt = "N"
aa[nt] = aa[nt] + 1
GC = (100.0 * (aa["G"] + aa["C"])) / len(seq)
np = NotePad()
tid = np.text_id()
tid.insert(
"end", "%s\n\n" %
(time.strftime("%y %b %d, %X\n", time.localtime(time.time()))) +
"Length = %d\nA=%d C=%d G=%d T=%d other=%d\nGC=%f\n\n" %
(len(seq), aa["A"], aa["C"], aa["G"], aa["T"], aa["N"], GC))
def Run(self):
self.notepad = NotePad()
tid = self.notepad.tid
self.notepad.menubar.configure(bg='red')
self.toplevel.destroy()
blastbg = xbb_blastbg.BlastDisplayer(self.command, tid)
blastbg.RunCommand()
# indicate the finished run by changing color
try:
self.notepad.menubar.configure(bg='green4')
except:
pass
def oldRun(self):
self.notepad = NotePad()
self.notepad.menubar.configure(bg='red')
self.notepad.bind('<Destroy>', self.Exit)
self.Update()
print(self.command)
self.pipe = posix.popen(self.command)
while 1:
try:
char = self.pipe.read(1)
self.notepad.insert(END, char)
self.notepad.update()
except:
break
if not char:
break
try:
self.notepad.menubar.configure(bg='green')
except:
pass
def oldRun(self):
self.notepad = NotePad()
self.notepad.menubar.configure(bg='red')
self.notepad.bind('<Destroy>', self.Exit)
self.Update()
print(self.command)
self.pipe = os.popen(self.command)
while True:
try:
char = self.pipe.read(1)
self.notepad.insert(END, char)
self.notepad.update()
except:
break
if not char:
break
try:
self.notepad.menubar.configure(bg='green')
except:
pass
self.worker.shutdown()
del self.worker
class BlastWorker(threading.Thread):
def __init__(self, command):
self.com = command
queue = Queue.Queue(0)
self.queue = queue
threading.Thread.__init__(self)
self.finished = 0
print(dir(queue))
print(queue.queue)
def shutdown(self):
# GRRRR How do I explicitely kill a thread ???????
#self.queue.put(None)
del self.queue
def run(self):
print('running %s' % self.com)
os.system(self.com)
self.finished = 1
if __name__ == '__main__':
np = NotePad()
com = "blastall -d nr -i test.fas -p blastx"
test = BlastDisplayer(com, np.tid)
test.RunCommand()
class BlastIt:
def __init__(self, seq, parent=None):
self.seq = seq
self.parent = parent
self.toplevel = Toplevel(parent)
Pmw.initialise(parent)
self.GetBlasts()
self.Choices()
def GetBlasts(self):
pin, nin = [], []
try:
pin.extend(glob.glob(os.environ['BLASTDB'] + '/*.pin'))
except:
pass
pin.extend(glob.glob('*.pin'))
try:
nin.extend(glob.glob(os.environ['BLASTDB'] + '/*.nin'))
except:
pass
nin.extend(glob.glob('*.nin'))
self.pin = map(lambda x: os.path.splitext(x)[0], pin)
self.nin = map(lambda x: os.path.splitext(x)[0], nin)
def Choices(self):
self.GetBlasts()
self.cf = Frame(self.toplevel)
self.cf.pack(side=TOP, expand=1, fill=X)
self.dbs = Pmw.ComboBox(self.cf,
label_text='Blast Databases:',
labelpos='nw',
scrolledlist_items=self.nin + self.pin,
selectioncommand=self.Validate)
self.blasts = Pmw.ComboBox(self.cf,
label_text='Blast Programs:',
labelpos='nw',
scrolledlist_items=[
'blastn', 'blastp', 'blastx', 'tblastn',
'tblastx'
],
selectioncommand=self.Validate)
self.dbs.pack(side=LEFT, expand=1, fill=X)
self.blasts.pack(side=LEFT, expand=1, fill=X)
self.alternative_f = Frame(self.cf)
self.alternative = Entry(self.alternative_f)
self.alternative_f.pack(side=TOP, fill=X, expand=1)
self.alternative.pack(side=LEFT, fill=X, expand=1)
self.ok = Button(self.alternative_f, text='Run', command=self._Run)
self.ok.pack(side=RIGHT)
self.dbs.selectitem(0)
self.blasts.selectitem(0)
self.Validate()
def Validate(self, *args):
db = self.dbs.get()
prog = self.blasts.get()
color = 'red'
if (prog in ['blastn', 'tblastx', 'tblastn']) == (db in self.nin):
color = 'green'
elif (prog in ['blastp', 'blastx']) == (db in self.pin):
color = 'green'
self.dbs.component('entry').configure(bg=color)
self.blasts.component('entry').configure(bg=color)
def _Run(self):
alternative_command = self.alternative.get()
if len(alternative_command.strip()):
self.command = alternative_command.strip()
else:
db = self.dbs.get()
prog = self.blasts.get()
self.command = 'echo %s | nice blastall -d %s -p %s' % (self.seq,
db, prog)
self.Run()
def Update(self):
self.notepad.update()
#print '.',
self.notepad.after(1, self.Update)
def oldRun(self):
self.notepad = NotePad()
self.notepad.menubar.configure(bg='red')
self.notepad.bind('<Destroy>', self.Exit)
self.Update()
print(self.command)
self.pipe = posix.popen(self.command)
while 1:
try:
char = self.pipe.read(1)
self.notepad.insert(END, char)
self.notepad.update()
except:
break
if not char:
break
try:
self.notepad.menubar.configure(bg='green')
except:
pass
def Run(self):
self.notepad = NotePad()
tid = self.notepad.tid
self.notepad.menubar.configure(bg='red')
self.toplevel.destroy()
blastbg = xbb_blastbg.BlastDisplayer(self.command, tid)
blastbg.RunCommand()
# indicate the finished run by changing color
try:
self.notepad.menubar.configure(bg='green4')
except:
pass
def Exit(self, *args):
try:
self.pipe.close()
del (pipe)
except:
pass
self.notepad.destroy()
sys.exit(0)
class BlastIt:
def __init__(self, seq, parent=None):
self.seq = seq
self.parent = parent
self.toplevel = Toplevel(parent)
Pmw.initialise(parent)
self.GetBlasts()
self.Choices()
def GetBlasts(self):
pin, nin = [], []
try:
pin.extend(glob.glob(os.environ['BLASTDB'] + '/*.pin'))
except:
pass
pin.extend(glob.glob('*.pin'))
try:
nin.extend(glob.glob(os.environ['BLASTDB'] + '/*.nin'))
except:
pass
nin.extend(glob.glob('*.nin'))
self.pin = [os.path.splitext(x)[0] for x in pin]
self.nin = [os.path.splitext(x)[0] for x in nin]
def Choices(self):
self.GetBlasts()
self.cf = Frame(self.toplevel)
self.cf.pack(side=TOP, expand=1, fill=X)
self.dbs = Pmw.ComboBox(self.cf,
label_text='Blast Databases:',
labelpos='nw',
scrolledlist_items=self.nin + self.pin,
selectioncommand=self.Validate
)
self.blasts = Pmw.ComboBox(self.cf,
label_text='Blast Programs:',
labelpos='nw',
scrolledlist_items=['blastn', 'blastp', 'blastx', 'tblastn', 'tblastx'],
selectioncommand=self.Validate
)
self.dbs.pack(side=LEFT, expand=1, fill=X)
self.blasts.pack(side=LEFT, expand=1, fill=X)
self.alternative_f = Frame(self.cf)
self.alternative = Entry(self.alternative_f)
self.alternative_f.pack(side=TOP, fill=X, expand=1)
self.alternative.pack(side=LEFT, fill=X, expand=1)
self.ok = Button(self.alternative_f, text='Run',
command=self._Run)
self.ok.pack(side=RIGHT)
self.dbs.selectitem(0)
self.blasts.selectitem(0)
self.Validate()
def Validate(self, *args):
db = self.dbs.get()
prog = self.blasts.get()
color = 'red'
if (prog in ['blastn', 'tblastx', 'tblastn']) == (db in self.nin):
color = 'green'
elif (prog in ['blastp', 'blastx']) == (db in self.pin):
color = 'green'
self.dbs.component('entry').configure(bg=color)
self.blasts.component('entry').configure(bg=color)
def _Run(self):
alternative_command = self.alternative.get()
if len(alternative_command.strip()):
self.command = alternative_command.strip()
else:
db = self.dbs.get()
prog = self.blasts.get()
self.command = 'echo %s | nice blastall -d %s -p %s' % (self.seq, db, prog)
self.Run()
def Update(self):
self.notepad.update()
self.notepad.after(1, self.Update)
def oldRun(self):
self.notepad = NotePad()
self.notepad.menubar.configure(bg='red')
self.notepad.bind('<Destroy>', self.Exit)
self.Update()
print(self.command)
self.pipe = os.popen(self.command)
while True:
try:
char = self.pipe.read(1)
self.notepad.insert(END, char)
self.notepad.update()
except:
break
if not char:
break
try:
self.notepad.menubar.configure(bg='green')
except:
pass
def Run(self):
self.notepad = NotePad()
tid = self.notepad.tid
self.notepad.menubar.configure(bg='red')
self.toplevel.destroy()
blastbg = xbb_blastbg.BlastDisplayer(self.command, tid)
blastbg.RunCommand()
# indicate the finished run by changing color
try:
self.notepad.menubar.configure(bg='green4')
except:
pass
def Exit(self, *args):
try:
self.pipe.close()
del(self.pipe)
except:
pass
self.notepad.destroy()
sys.exit(0)
