#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""rna_rosetta_check_progress.py - check progress for many simulations of Rosetta
Example::
[peyote2] rosetta_jobs rna_rosetta_check_progress.py .
jobs #curr #todo #decoys done
0 ./rp17s223 200 0 407 [ ]
1 ./rp17hcf 0 0 0 [ ]
# curr 232 #todo 0
"""
from __future__ import print_function
import subprocess
import os
import pandas as pd
import glob
import sys
import argparse
try:
from rna_tools.rna_tools_config import RNA_ROSETTA_RUN_ROOT_DIR_MODELING, RNA_ROSETTA_NSTRUC
except:
print('Set up RNA_ROSETTA_RUN_ROOT_DIR_MODELING in rna_tools.rna_tools_config_local.py')
from rna_tools.rna_tools_config import EASY_CAT_PATH
# print('Set up EASY_CAT_PATH in rpt_config_local.py')
print(EASY_CAT_PATH)
[docs]
def run_cmd(cmd):
o = subprocess.Popen(
cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
out = o.stdout.read().strip().decode()
err = o.stderr.read().strip().decode()
return out, err
[docs]
def get_parser():
parser = argparse.ArgumentParser(
description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('dir', default=RNA_ROSETTA_RUN_ROOT_DIR_MODELING,
help="""directory with rosetta runs, define by RNA_ROSETTA_RUN_ROOT_DIR_MODELING
right now: \n""" + RNA_ROSETTA_RUN_ROOT_DIR_MODELING)
parser.add_argument('-v', '--verbose',
action='store_true', help="be verbose")
parser.add_argument('-m', '--min-only', action='store_true',
help="check only for mo folder")
parser.add_argument('-s', '--select',
help="select for analysis only jobs with this phrase, .e.g., evoseq_", default='')
parser.add_argument('-k', '--kill', action='store_true', help="""kill (qdel) jobs if your reach
limit (nstruc) of structure that you want, right now is %i structures""" % RNA_ROSETTA_NSTRUC)
return parser
if __name__ == '__main__':
args = get_parser().parse_args()
v = args.verbose
# jobs = [x.replace('.fa','') for x in glob.glob( '*.fa')] # sys.argv[1] +
# sys.argv[1] +
# print jobs
jobs = [x for x in glob.glob(args.dir + '/*')]
if v:
print(jobs)
curr_path = os.getcwd()
d = {}
d['#decoys'] = []
d['jobs'] = []
d['#curr'] = []
d['#todo'] = []
d['done'] = []
d['progress'] = []
for j in jobs:
if args.select:
if not args.select in j:
continue
if v:
print(j)
d['jobs'].append(j)
try:
os.chdir(j)
except:
pass # OSError: [Errno 20] Not a directory:
dirs = []
if not args.min_only:
# Uff.. this is crazy.
for c in ['_', '__', '___', 'x', 'y', 'z', 'X', 'Y', 'Z', 'o', 'out'] + ['r' + str(i) for i in range(0, 1000)]:
if os.path.exists(c):
dirs.append(c)
# print ' ', j, '', dirs
cmd = EASY_CAT_PATH + ' ' + ' '.join(dirs)
if v:
print('cmd: %s' % cmd)
out, err = run_cmd(cmd)
if out.strip():
if len(j) <= 5:
if v:
print(out + '\t\t', end='')
else:
if v:
print(out + '\t', end='')
no_decoys = int(out.split()[-2])
else:
no_decoys = 0
if v:
print('#', no_decoys)
else:
# # of minimized
RNA_ROSETTA_NSTRUC = 1600 # change expected !!!! pretty ugly
for c in ['mo']:
if os.path.exists(c):
dirs.append(c)
# print ' ', j, '', dirs
cmd = EASY_CAT_PATH + ' ' + ' '.join(dirs)
if v:
print(cmd)
out, err = run_cmd(cmd)
if out.strip():
if len(j) <= 5:
if v:
print(out + '\t\t', end='')
else:
if v:
print(out + '\t', end='')
no_decoys = int(out.split()[-2])
else:
no_decoys = 0
if v:
print('#', no_decoys)
# check current running, only 6 char are taken from dir name
# /home/magnus/rosetta_jobs/rp17s223 -> rp17s2199, rp17s2185
cmd = 'qstat | grep ' + \
os.path.basename(j)[:6] + ' | grep " r " | wc -l '
if v:
print(cmd)
out, err = run_cmd(cmd)
if v:
print('@cluster #curr ', out, end="")
curr = int(out)
d['#curr'].append(curr)
# check todo
out, err = run_cmd('qstat | grep ' + os.path.basename(j)
[:6] + ' | grep " qw " | wc -l ')
if v:
print('#todo ', out, end="")
todo = int(out)
d['#todo'].append(todo)
d['#decoys'].append(no_decoys)
if no_decoys >= RNA_ROSETTA_NSTRUC:
if v:
print('# @cluster:', out, ' < ............... OK')
d['done'].append('[x]')
if args.kill:
cmd = 'qstat | grep ' + \
os.path.basename(j)[:6] + \
" | awk '{print $1}' | xargs qdel "
print(cmd)
os.system(cmd)
else:
d['done'].append('[ ]')
if v:
print('# @cluster:', out)
# cmd = 'kill '
# print cmd
d['progress'].append(round((float(no_decoys) / 10000) * 100, 2))
os.chdir(curr_path)
df = pd.DataFrame(d, columns=['jobs', '#curr', '#todo', '#decoys', 'done', 'progress'])
print(df)
out, err = run_cmd('qstat | grep magnus | grep " r " | wc -l ')
print('#curr ', out, end=" ")
out, err = run_cmd('qstat | grep magnus | grep " qw " | wc -l ')
print('#todo ', out)