Source code for rna_tools.tools.rna_rosetta.rna_rosetta_n

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""rna_roseta_n.py - show me # of structure in a silent file

Example::

     $ rna_rosetta_n.py ade.out
     21594

"""
from __future__ import print_function
import subprocess
import argparse


[docs]def get_parser(): parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) parser.add_argument('-v', '--verbose', action='store_true') parser.add_argument('file', help='ade.out') return parser
[docs]def get_no_structures(file): p = subprocess.Popen('cat ' + file + ' | grep SCORE | wc -l', shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) stderr = p.stderr.read().strip() if stderr: print(stderr) return int(p.stdout.read().strip()) - 1
[docs]def run(): """Pipline for modeling RNA.""" args = get_parser().parse_args() ns = get_no_structures(args.file) if args.verbose: print(args.file.ljust(30), end='') print(ns)
# main if __name__ == '__main__': run()