#!/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
$ rna_rosetta_n.py *out
default.out 100
default1.out 200
default2.out 200
default3.out 100
"""
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('-0', '--zero', action='store_true')
parser.add_argument('file', help='ade.out', nargs='+')
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(f):
"""Pipline for modeling RNA."""
args = get_parser().parse_args()
import os
if os.path.isfile(f):
ns = get_no_structures(f)
if args.verbose:
# print(args.file.ljust(30), end='')
print(f, ns)
else:
print(ns)
else:
if args.zero:
print(0)
else:
print(f, 'missing')
# main
if __name__ == '__main__':
parser = get_parser()
args = parser.parse_args()
if list != type(args.file):
args.file = [args.file]
for f in args.file:
run(f)