#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Convert a secondary structure with a pk to the SimRNA format::
rna_convert_pseudoknot_formats git:(master) ✗ python rna_ss_pk_to_simrna.py test_data/ss_with_pk.ss
((((([[[[[[)))))........(.((....(]]]]]].)..(((. .)))...)).)
(((((......)))))........(.((....(.......)..(((. .)))...)).)
.....((((((......................))))))........ ...........
"""
import argparse
SECOND_PK_CHAR = ['{', '}']
[docs]
def is_pk(ss):
if ss.find('[') > -1:
return True
if ss.find(']') > -1:
return True
[docs]
def get_multiple_lines(ss):
ss_n = ''
ss_pk = ''
for i in ss.strip():
if i == '[':
j = '('
i = '.'
elif i == ']':
j = ')'
i = '.'
elif i == ' ': # not space
j = ' '
else:
j = '.'
ss_n += i
ss_pk += j
return ss_n + '\n' + ss_pk
[docs]
def get_parser():
parser = argparse.ArgumentParser()
parser.add_argument('file', help='file')
return parser
if __name__ == '__main__':
parser = get_parser()
args = parser.parse_args()
if args.file:
ss = open(args.file).readline()
print(ss)
if is_pk(ss):
print((get_multiple_lines(ss)))
else:
print(ss)