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 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 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 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 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 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))
