#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Secondary structure analysis"""
import os
import tempfile
import shutil
import subprocess
from rna_tools.rna_tools_config import VARNA_JAR_NAME, VARNA_PATH
[docs]
class ExceptionOpenPairsProblem(Exception):
pass
[docs]
def draw_ss(title, seq, ss, img_out, resolution=4, verbose=False):
"""Draw Secondary Structure using VARNA (you need correct configuration for this).
If everything is OK, return None, if an error (=exception) return stderr.
Usage::
>>> seq = 'GGAAACC'
>>> ss = '((...))'
>>> img_out = 'output/demo.png'
>>> draw_ss('rna', seq, ss, img_out)
>>> print('Made %s' % img_out)
Made output/demo.png
.. image:: ../../rna_tools/output/demo.png
:scale: 25 %
Can be used with http://geekbook.readthedocs.io/en/latest/rna.html"""
curr = os.getcwd()
os.chdir(VARNA_PATH) # VARNAv3-93-src')
if verbose:
print(VARNA_PATH)
t = tempfile.NamedTemporaryFile(delete=False)
t.name += '.png'
cmd = 'java -cp ' + VARNA_JAR_NAME + ' fr.orsay.lri.varna.applications.VARNAcmd -sequenceDBN ' + seq + \
" -structureDBN '" + ss + "' -o " + t.name + " -title '" + \
title + "' -resolution '" + str(resolution) + "'"
if verbose:
print(cmd)
p = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
p.wait()
out = p.stderr.read().decode().strip()
os.chdir(curr)
if out.find('Exception') > -1:
return out
else:
if verbose:
print(t.name)
shutil.move(t.name, img_out)
[docs]
def parse_vienna_to_pairs(ss, remove_gaps_in_ss=False):
"""Parse Vienna (dot-bracket notation) to get pairs.
Args:
ss (str): secondary stucture in Vienna (dot-bracket notation) notation
remove_gaps_in_ss (bool): remove - from ss or not, design for DCA (tpp case
``ss = "(((((((((.((((.(((.....))))))......------)....."``
works with pk of the first level, ``[[]]``
Returns:
list of two lists: (pairs, pairs_pk)
Examples::
>>> parse_vienna_to_pairs('((..))')
([[1, 6], [2, 5]], [])
>>> parse_vienna_to_pairs('(([[))]]')
([[1, 6], [2, 5]], [[3, 8], [4, 7]])
>>> parse_vienna_to_pairs('((--))')
([[1, 6], [2, 5]], [])
>>> parse_vienna_to_pairs('((--))', remove_gaps_in_ss=True)
([[1, 4], [2, 3]], [])
>>> parse_vienna_to_pairs('((((......')
Traceback (most recent call last):
File "/usr/lib/python2.7/doctest.py", line 1315, in __run
compileflags, 1) in test.globs
File "<doctest __main__.parse_vienna_to_pairs[4]>", line 1, in <module>
parse_vienna_to_pairs('((((......')
File "./SecondaryStructure.py", line 106, in parse_vienna_to_pairs
raise ExceptionOpenPairsProblem('Too many open pairs (()) in structure')
ExceptionOpenPairsProblem: Too many open pairs (()) in structure
"""
if remove_gaps_in_ss:
ss = ss.replace('-', '')
stack = []
pairs = []
pairs_pk = []
stack_pk = []
for c, s in enumerate(ss):
if s == '(':
stack.append(c + 1)
if s == ')':
pairs.append([stack.pop(), c + 1])
if s == '[':
stack_pk.append(c + 1)
if s == ']':
pairs_pk.append([stack_pk.pop(), c + 1])
if stack:
raise ExceptionOpenPairsProblem('Too many open pairs (()) in structure')
if stack_pk:
raise ExceptionOpenPairsProblem('Too many open pairs [[]] in structure')
pairs.sort()
pairs_pk.sort()
return(pairs, pairs_pk)
# main
if __name__ == '__main__':
import doctest
doctest.testmod()