def translate(self):
input_seq = self.ui.text_input.toPlainText()
try:
dna_instance = dna(seq=input_seq, type=self.type)
self.ui.textEdit_console.clear()
self.ui.textEdit_console.insertPlainText(
dna_instance.translate_seq())
self.ui.textEdit_console.moveCursor(qtg.QTextCursor.Start)
except:
self.invalid()
def random_seq(self):
dna_instance = dna()
if self.ui.textEdit_length.text():
length = int(self.ui.textEdit_length.text())
dna_instance.generate_random(length=length,
new_type=str(self.type))
else:
dna_instance.generate_random(new_type=self.type)
self.ui.text_input.clear()
self.ui.text_input.insertPlainText(dna_instance.seq)
self.ui.text_input.moveCursor(qtg.QTextCursor.Start)
def read_frames(self):
input_seq = self.ui.text_input.toPlainText()
try:
dna_instance = dna(seq=input_seq, type=self.type)
reading_frames = "[Open reading frames]:\n\n"
for i, j in zip(dna_instance.open_reading_frames(), range(1, 7)):
reading_frames += f"[{j}]: {i}\n\n"
self.ui.textEdit_console.clear()
self.ui.textEdit_console.insertPlainText(reading_frames)
self.ui.textEdit_console.moveCursor(qtg.QTextCursor.Start)
except:
self.invalid()
def seq_info(self):
input_seq = self.ui.text_input.toPlainText()
input_label = self.ui.textEdit_label.text()
try:
dna_instance = dna(seq=input_seq,
type=self.type,
label=input_label)
self.ui.textEdit_console.clear()
self.ui.textEdit_console.insertPlainText(
dna_instance.get_info() + '\n[GC content]: ' +
str(dna_instance.gc_content()) + '%')
self.ui.textEdit_console.moveCursor(qtg.QTextCursor.Start)
except:
self.invalid()
def proteinsORF(self):
input_seq = self.ui.text_input.toPlainText()
try:
dna_instance = dna(seq=input_seq, type=self.type)
proteins_found = dna_instance.proteins_rf()
num_proteins = len(proteins_found)
prots = f"[Proteins from all open reading frames]: Found {num_proteins} proteins\n\n"
for i, j in zip(proteins_found, range(1, num_proteins + 1)):
prots += f"[{j}]: {i}\n\n"
self.ui.textEdit_console.clear()
self.ui.textEdit_console.insertPlainText(prots)
self.ui.textEdit_console.moveCursor(qtg.QTextCursor.Start)
except:
self.invalid()
#!/usr/bin/env python
from double_helix import double_helix as dna
from utilities import read_FASTA, read_textfile, write_textfile
test_seq = dna()
test_seq.generate_random(40, 'RNA')
for rf in test_seq.open_reading_frames():
write_textfile('rfs.txt', rf, 'a')