#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""rna_roseta_head.py - get a head of a Rosetta silent file.
Example::
$ rna_rosetta_head.py -n 10000 thf.out
# a new file will be created, thf_10000.out
Silent file::
[peyote2] thf head -n 100 thf.out
SEQUENCE: ggagaguagaugauucgcguuaagugugugugaaugggaugucgucacacaacgaagcgagagcgcggugaaucauugcauccgcucca
SCORE: score rna_data_backbone rna_vdw rna_base_backbone rna_backbone_backbone rna_repulsive rna_base_pair rna_base_axis rna_base_stagger rna_base_stack rna_base_stack_axis rna_rg atom_pair_constraint linear_chainbreak N_WC N_NWC N_BS description
REMARK BINARY SILENTFILE
SCORE: -601.975 0.000 31.113 -16.960 -3.888 20.501 -302.742 -38.531 -158.004 -80.764 -110.053 23.750 0.000 33.601 32 6 86 S_000001_000
FOLD_TREE EDGE 1 4 -1 JEDGE 4 85 1 C4 C2 END EDGE 4 5 -1 EDGE 85 80 -1 EDGE 85 89 -1 JEDGE 80 40 5 C4 C2 END EDGE 80 78 -1 EDGE 40 43 -1 EDGE 40 33 -1 JEDGE 33 45 4 C4 C2 END EDGE 45 54 -1 EDGE 45 44 -1 EDGE 33 20 -1 JEDGE 20 65 3 C2 C4 END EDGE 65 67 -1 EDGE 20 17 -1 EDGE 65 63 -1 JEDGE 17 69 2 C4 C2 END JEDGE 63 58 6 C4 C2 END EDGE 17 6 -1 EDGE 58 59 -1 EDGE 63 60 -1 EDGE 69 77 -1 EDGE 58 55 -1 EDGE 69 68 -1 S_000001_000
RT -0.987743 0.139354 0.0703103 0.135963 0.989404 -0.0509304 -0.0766626 -0.0407466 -0.996224 6.25631 0.103544 0.0647696 S_000001_000
RT -0.98312 0.1587 -0.091045 0.166923 0.981743 -0.0912024 0.074909 -0.10486 -0.991662 5.89962 -1.95819 -0.1075 S_000001_000
RT -0.987645 0.154078 0.0285994 0.153854 0.988044 -0.00989514 -0.0297821 -0.00537275 -0.999542 6.13138 1.047 0.115722 S_000001_000
RT -0.989884 0.140722 0.0180554 0.140036 0.989532 -0.0348618 -0.0227723 -0.0319807 -0.999229 6.21787 0.201588 -0.0264223 S_000001_000
RT -0.988455 0.134013 0.0706914 0.134924 0.990822 0.00825457 -0.0689364 0.0176973 -0.997464 6.19447 0.189237 0.125791 S_000001_000
RT -0.990412 0.138036 0.00546261 0.137927 0.990299 -0.0168644 -0.00773751 -0.0159492 -0.999843 6.25456 0.0842849 -0.0135807 S_000001_000
ANNOTATED_SEQUENCE: g[RGU:LowerRNA:Virtual_Phosphate]gaga[RAD:rna_cutpoint_lower]g[RGU:rna_cutpoint_upper]uagaugauucgcguuaagugugugugaaugggauguc[RCY:rna_cutpoint_lower]g[RGU:rna_cutpoint_upper]ucacacaacg[RGU:rna_cutpoint_lower]a[RAD:rna_cutpoint_upper]agcg[RGU:rna_cutpoint_lower]a[RAD:rna_cutpoint_upper]gagcgcg[RGU:rna_cutpoint_lower]g[RGU:rna_cutpoint_upper]ugaaucauu[URA:rna_cutpoint_lower]g[RGU:rna_cutpoint_upper]cauccgcucca[RAD:UpperRNA] S_000001_000
Le3nY9smsa4zEMGdvAA+z+e
It seems to work::
-rw-rw-r-- 1 magnus users 474M 2017-08-06 05:25 thf_10000.out
-rw -rw-r-- 1 magnus users 947M 2017-08-06 04:54 thf.out
[peyote2] thf rna_rosetta_n.py thf_10000.out
10000
"""
from __future__ import print_function
import subprocess
import argparse
import sys
[docs]
def get_parser():
parser = argparse.ArgumentParser(
description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('-v', '--verbose', action='store_true')
parser.add_argument('-n', '--nstruc', type=int, default=10000)
parser.add_argument('file', help='ade.out')
return parser
[docs]
def run():
"""Pipline for modeling RNA."""
args = get_parser().parse_args()
nfile = ''
c = -2
for l in open(args.file):
# print(l)
if l.startswith('SCORE'):
c += 1
if c == int(args.nstruc):
f = open(args.file.replace('.out', '_' + str(args.nstruc) + '.out'), 'w')
# print(nfile)
f.write(nfile)
f.close()
sys.exit(1)
nfile += l
# main
if __name__ == '__main__':
run()