def _tag_select(mode): tag = input('Input tag: ').strip() if tag == '' or tag == 'None': tag == 'None' else: if tag in tagset: pass #Just a pass. Do not implement anything. elif tag.upper() in ('HIS6', 'HIS-TAG', 'HISTAG', 'POLYHISTIDINE'): tag = 'His6' else: print('Warning:invalid tag name...') yn = input('Wish to handle the input as sequence literal? (y/n): ') if yn == 'y': comset = mode_set(mode) temp_tag = '' for char in tag: if char in comset: temp_tag += char else: print( 'Warning:Character \'' + char + '\' is not a valid character in current mode and was ignored.' ) tag = temp_tag else: tag = _tag_select(mode) return tag
def _tag_select(self, mode): tag = self.buttonGroup.checkedButton().text()[2:].strip() if tag == 'Other sequence:': tag = self.text_tag.toPlainText() comset = mode_set(mode) temp_tag = '' check_err = 0 for char in tag: if char in comset: temp_tag += char else: check_err += 1 err_tag = ' ' + str(check_err) + ' INVALID CHARACTER(s) WERE IGNORED' tag = temp_tag self.wrn_tag.setText(err_tag) return tag
def _dna_select(self, dna, mode): lines = dna.split('\n') comset = mode_set(mode) out = [] started = False temp_header = '' temp_seq = [] temp_seq_list = [] for line in lines: line_lstrip = line.lstrip() if line_lstrip.strip() == '': continue elif line_lstrip[0] == '>': if started: if temp_seq_list == []: break else: temp_seq = ''.join(temp_seq_list) out.append((temp_header, temp_seq)) else: started = True temp_header = line[1:].rstrip() temp_seq_list = [] elif line_lstrip[0] == ';': continue else: l = line_lstrip.strip().upper() for i in range(len(l)): if l[i] in comset: temp_seq_list.extend(l[i]) elif l[i].isalpha(): continue else: print('Error: character \"' + l[i] + '\" does not match with specified type \"' \ + mode + '\" in function fasta_reader(' + dna + ').') temp_seq = ''.join(temp_seq_list) out.append((temp_header, temp_seq)) print(lines) return out
def _tag_select(self, mode): tag = self.buttons_tag.checkedButton().text() if tag == 'Other:': tag = self.text_tag.toPlainText() comset = mode_set(mode) temp_tag = '' check_err = 0 for char in tag: if char in comset: temp_tag += char else: check_err += 1 self.popup_err(' ' + str(check_err) + ' INVALID CHARACTER(s) WERE IGNORED IN CUSTOM TAG') tag = temp_tag elif tag == 'His-Tag': tag = 'His6' else: tag = '' return tag