Source code for

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""A tool to calc inf_all, inf_stack, inf_WC, inf_nWC, SNS_WC, PPV_WC, SNS_nWC, PPV_nWC between two structures.

Mind, that ClaRNA is pretty slow, it takes even a few seconds to analyze a structure,
so for, say, 1000 models you need a few hours.

How to make it faster? 

First, you can use ``--number-of-threads`` to specify the number of cores used for multiprocessing.

Second, the procedure implemented in here is composed of two steps, first for each structure ClaRNA is used to generate an output with contacts, then these files are used for comparisons. So, if you want to re-run your analysis, you don't have to re-run ClaRNA itself. Thus, be default ClaRNA is not executed if <model>.outCR is found next to the analyzed files.  To change this behavior, force (``--force``) to re-run ClaRNA.

from __future__ import print_function

import progressbar
import argparse
import sys
import os
import subprocess
import re
import tempfile
import csv
import shutil

import warnings
warnings.simplefilter(action='ignore', category=FutureWarning)

from multiprocessing import Pool, Lock, Value, Process
from import clarna_app
#from rna_tools.opt.BasicAssessMetrics.BasicAssessMetrics import InteractionNetworkFidelity

import pandas as pd
pd.set_option('display.max_rows', 1000)

[docs]def get_parser(): parser = argparse.ArgumentParser()#usage="%prog [<options>] <pdb files (test_data/*)>") parser.add_argument('-t',"--target_fn", dest="target_fn", default='', help="pdb file") parser.add_argument('-m',"--number-of-threads", dest="nt", default=3, help="number of threads used for multiprocessing, if 1 then mp is not used \ (useful for debugging)!") parser.add_argument('--ignore-files', help='files to be ingored, .e.g, \'solution\'', default='') parser.add_argument('-s',"--ss", dest="ss", default='', help="A:(([[))]], works only for single chain (the chain is A by default)") parser.add_argument('--no-stacking', action="store_true", help="default: use stacking, if this option on, don't take into account stacking, \n\nWARNING/BUG: inf_all will be incorrectly calculated if stacking is off") parser.add_argument('--debug', action="store_true") parser.add_argument('-pr', '--print-results', action="store_true") parser.add_argument('-sr', '--sort-results', action="store_true") parser.add_argument('--method', default="clarna", help="you can use mcannotate* or clarna (right now only clarna is tested)") parser.add_argument("--target-selection", default='', help="selection, e.g. A:10-16+20, where #16 residue is included") parser.add_argument("--model-selection", default='', help="selection, e.g. A:10-16+20, where #16 residue is included") parser.add_argument('--renumber-residues', help='renumber residues from 1 to X for comparison with selection', default='', action="store_true") parser.add_argument('--dont-remove-sel-files', action="store_true", help="don't remove temp files created based on target|model-selectionforce") parser.add_argument('-f',"--force", dest="force", action="store_true", help="force to run ClaRNA even if <pdb>.outCR file is there, for will be auto True when selection defined") parser.add_argument('-v',"--verbose", dest="verbose", action="store_true", help="be verbose, tell me more what're doing") parser.add_argument('-o',"--out_fn", dest="out_fn", default='inf.csv', help="out csv file, be default `inf.csv`") parser.add_argument('files', help="files, .e.g folder_with_pdbs/*pdbs", nargs='+') return parser
# Prepare the lock and the counter for MP from ctypes import c_int lock = Lock() counter = Value(c_int)
[docs]def do_job(i, method='clarna'): """Run ClaRNA & Compare, add 1 to the counter, write output to csv file (keeping it locked)""" #if method == 'clarna': # run clarna & compare # ugly hack for direct import try: args.force args.no_stacking except NameError: force = True no_stacking = False else: force = args.force no_stacking = args.no_stacking i_cl_fn = clarna_app.clarna_run(i, force, not no_stacking) output = clarna_app.clarna_compare(target_cl_fn,i_cl_fn, verbose=DEBUG) if args.verbose: print(output) ## else: ## rmsd, DI_ALL, INF_ALL, INF_WC, INF_NWC,INF_STACK = InteractionNetworkFidelity(os.path.abspath(target_fn), ## '/tmp/empty-index', ## os.path.abspath(i), ## '/tmp/empty-index') ## if args.debug: ## print(rmsd) # counter and bar global counter counter.value += 1 bar.update(counter.value) # write csv lock.acquire() # take only filename of target cells = output.split() cells[0] = os.path.basename(cells[0]) csv_writer.writerow(cells) csv_file.flush() lock.release()
#main if __name__ == '__main__': parser = get_parser() args = parser.parse_args() DEBUG = False if args.debug: DEBUG = True args.verbose = True print(args) if len(sys.argv) == 1: print((parser.print_help())) sys.exit(1) input_files = args.files #################################### # implement ignore files tmp = [] if args.ignore_files: for f in input_files: if args.ignore_files in f: continue tmp.append(f) input_files = tmp if args.model_selection or args.target_selection: args.force = True if args.model_selection: tmp = [] for f in input_files: new_f = f.replace('.pdb', '_sel.pdb') cmd = " --extract '" + args.model_selection + "' " + f + ' > ' + new_f os.system(cmd) if args.renumber_residues: cmd = " --no-hr --rpr --inplace --renumber-residues " + new_f os.system(cmd) tmp.append(new_f) input_files = tmp target_fn = args.target_fn if args.target_selection: new_target_fn = target_fn.replace('.pdb', '_sel.pdb') cmd = " --extract '" + args.target_selection + "' " + target_fn + ' > ' + new_target_fn os.system(cmd) if args.renumber_residues: cmd = " --no-hr --rpr --inplace --renumber-residues " + new_target_fn os.system(cmd) target_fn = new_target_fn ss = if ss: # generate target_fn ss_txt = open(ss).read().split('\n')[2] target_cl_fn = clarna_app.get_ClaRNA_output_from_dot_bracket(ss_txt, temp=False) else: target_cl_fn = clarna_app.clarna_run(target_fn, args.force) # keep target save, don't overwrite it when force and # target is in the folder that you are running ClaRNA on # /tmp/tmp2nmeVB/1i6uD_M1.pdb.outCR d = tempfile.mkdtemp() tmp_target_cl_fn = d + os.sep + os.path.basename(target_cl_fn) shutil.copyfile(target_cl_fn, tmp_target_cl_fn) target_cl_fn = tmp_target_cl_fn out_fn = args.out_fn if args.no_stacking: print('WARNING/BUG: inf_all will be incorrectly calculated if stacking is off') # Open output file csv_file = open(out_fn, 'w') csv_writer = csv.writer(csv_file, delimiter=',') csv_writer.writerow('target,fn,inf_all,inf_stack,inf_WC,inf_nWC,sns_WC,ppv_WC,sns_nWC,ppv_nWC'.split(',')) csv_file.flush() # Init bar and to the job try: bar = progressbar.ProgressBar(max_value=len(input_files)) bar.update(0) except TypeError: print('Please install progressbar2 (not progressbar), e.g. pip install progressbar2') sys.exit(1) # Main meat number_processes = int(args.nt) open('/tmp/empty-index', 'a').close() ## ugly hack if number_processes > 1: # multi p = Pool(number_processes), input_files) # , args.method) else: # single process for c, i in enumerate(input_files):#, range(len(input_files))): do_job(i, args.method) print('\ncsv was created! ', out_fn) # hack with pandas csv_file.close() df = pd.read_csv(out_fn) df = df.round(2) df['target'] = df['target'].str.replace('.outCR', '') df['fn'] = df['fn'].str.replace('.outCR', '') if args.sort_results: df = df.sort_values('inf_all', ascending=False) if args.print_results: print(df)#.to_html()) #df.replace(' ', '&nsbp')) df.to_csv(out_fn, sep=',', index=False) # remove temp files if not args.dont_remove_sel_files: if args.target_selection: os.remove(os.path.abspath(target_fn)) if args.model_selection: for f in input_files: if f == target_fn: continue os.remove(os.path.abspath(f))