#!/usr/bin/env python
"""
Usage::
$ rna_clarna_app.py ../../input/5k7c_clean_onechain_renumber_as_puzzle_srr.pdb \
../../input/5k7c_clean_onechain_renumber_as_puzzle_srr.pdb
((((([[[[[[)))))........(.((....(]]]]]].)..(((......)))...)).)
Example:
.. code-block:: python
from rna_tools.utils.clarna_app import clarna_app
if __name__ == '__main__':
ss = '((((.[[[[[[.))))........((((.....]]]]]]...(((((....)))))..))))'
fnCRref = clarna_app.get_ClaRNA_output_from_dot_bracket(ss)
f = '../rna_calc_rmsd/test_data/pistol/5k7c_clean_onechain_renumber_as_puzzle_srr.pdb'
fnCR = clarna_app.clarna_run(f, force=False)
results = clarna_app.clarna_compare(fnCRref, fnCR)
print results #
#tmp_Z42i_..pdb.outCR 5k7c_clean_onechain_renumber_as_puzzle_srr.pdb.outCR 0.706 NA 0.865 NA 0.842 0.889 NA 0.000
"""
import argparse
import subprocess
import sys
import os
import tempfile
from rna_tools.tools.rna_convert_pseudoknot_formats.rna_pk_simrna_to_one_line import get_one_line
[docs]
def clarna_run(fn, force=True, stacking=True, verbose=False):
"""Run ClaRNA run
Args:
fn (str): filename to analyze
Return:
str: a filename to ClaRNA output (fn + '.outCR')"""
if verbose:
print('stacking', stacking)
fn_out = fn + '.outCR'
if os.path.isfile(fn_out) and not force:
pass
else:
opts = ''
if stacking:
opts = ' -bp+stack '
cmd = 'rna_clarna_run.py ' + opts + ' -ipdb ' + fn + ' > ' + fn_out
if verbose: print(cmd)
os.system(cmd)
if os.stat(fn_out).st_size == 0: # if file is empty also run
cmd = 'rna_clarna_run.py -bp+stack -ipdb ' + fn + ' > ' + fn_out
if verbose: print(cmd)
os.system(cmd)
return fn_out
[docs]
def get_dot_bracket_from_ClaRNAoutput(inCR, verbose=False):
"""In inCR file
.. warning:: This function requres 'ClaRNAwd_to_vienaSS' contact marcin.magnus@icloud.com """
cmd = ClaRNA_play_path + '/lib/ClaRNAwd_to_vienaSS/ClaRNAwd_output_parser_get_SS ' + inCR
o = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
std = o.stdout.read().strip()
if verbose: std
return std
[docs]
def clarna_compare(target_cl_fn,i_cl_fn, verbose=False):
"""Run ClaRNA compare (from rna_tools/tools/clarna_play).
:return: a list target, fn, scores
Scores::
inf_all 0.706
inf_stack -999.999 -> NA
inf_WC 0.865
inf_nWC -999.999 -> NA
SNS_WC 0.842
PPV_WC 0.889
SNS_nWC NA
PPV_nWC 0.000
Example of the list::
5k7c_clean_onechain_renumber_as_puzzle_srr.pdb pistol_thrs0.50A_clust01-000001_AA.pdb
0.642 NA 0.874 0.000 0.944 0.810 0.000 0.000s
use ``results.split()[4]`` to get inf_WC"""
cmd = 'rna_clarna_compare.py -iref ' + target_cl_fn + ' -ichk ' + i_cl_fn
if verbose: print('clarna_app::cmd', cmd)
o = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
std = o.stdout.read().strip().decode()
if not std:
raise Exception('ClaRNA output is empty, something went wrong:\n\t %s \n %s' % (cmd, std))
if verbose:
print('clarna_app::o.stderr', o.stderr.read())
#WARNING: nWC has more than one values struc/1i6uD_M425.pdb.outCR: ['SW_tran', 'WW_tran']
#WARNING: nWC has more than one values struc/1i6uD_M425.pdb.outCR: ['SW_tran', 'WW_tran']
#1i6uD_M1.pdb.outCR 1i6uD_M425.pdb.outCR 0.707 0.000 0.756 0.500 0.571 1.000 0.250 1.000
return std.split('\n')[-1] # solution for this ^, keep the clarna_compare quite
[docs]
def get_ClaRNA_output_from_dot_bracket(ss, temp=True, verbose=False):
"""
Get dummy ClaRNA output out of dat bracket secondary structure (ss)
Args:
ss (string): secondary structure
Return:
a filename to ClaRNA output"""
from rna_tools.SecondaryStructure import parse_vienna_to_pairs
if ss.find(':') > -1:
chain,ss = ss.split(':')
else:
chain = 'A'
ss = ss
pairs, pairs_pk = parse_vienna_to_pairs(ss, remove_gaps_in_ss=False)
pairs += pairs_pk
txt = 'Classifier: Clarna\n'
txt += 'chains: A 1 ' + str(len(ss)) + '\n'
for bp in pairs:
txt += '%s %i %s %i bp G C WW_cis 1 \n' % (chain, bp[0], chain, bp[1])
if verbose: print(txt.strip())
if temp:
f = tempfile.NamedTemporaryFile()
name = f.name
else:
name = 'target'
foutCR = name + '.pdb.outCR'
if verbose: print(foutCR)
ft = open(foutCR, 'w')
ft.write(txt)
ft.close()
return foutCR
[docs]
def get_parser():
parser = argparse.ArgumentParser()#usage="%prog [<options>] <pdb files (test_data/*)>")
parser.add_argument('files', help="files", nargs='+')
parser.add_argument('-f',"--force",
dest="force",
action="store_true",
help="force to run ClaRNA")
parser.add_argument('-v',"--verbose",
dest="verbose",
action="store_true",
help="verbose")
return parser
# main
if __name__ == '__main__':
parser = get_parser()
args = parser.parse_args()
if len(sys.argv) == 1:
print(parser.print_help())
sys.exit(1)
for f in args.files:
print(f)
fn_out = clarna_run(f, args.force)
mdb = get_dot_bracket_from_ClaRNAoutput(fn_out, args.verbose) # multie line dot bracket
db = get_one_line(mdb.split('\n'))
print(db)