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