Source code for rna_pdb_tools.SecondaryStructure

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Secondary structure analysis"""

import os
import tempfile
import shutil
import subprocess

from rna_pdb_tools.rpt_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_pdb_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()