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#!/usr/bin/env python
# Author: Duy Tin Truong (duytin.truong@unitn.it)
# at CIBIO, University of Trento, Italy
import subprocess
import os
import multiprocessing
from multiprocessing.pool import ThreadPool
import sys
import cStringIO
from tempfile import NamedTemporaryFile
import which
import functools
import traceback
import numpy
class ooSubprocessException(Exception):
pass
class ooSubprocess:
def __init__(self, tmp_dir='tmp/'):
self.chain_cmds = []
self.tmp_dir = tmp_dir
mkdir(tmp_dir)
def ex(
self,
prog,
args=[],
get_output=False,
get_out_pipe=False,
out_fn=None,
in_pipe=None,
verbose=True,
**kwargs):
if not which.is_exe(prog):
raise ooSubprocessException('Error: cannot find the program %s '\
'in the executable path!'%prog)
if isinstance(args, str):
args = args.split()
if not isinstance(args, list):
args = [args]
cmd = [prog] + args
print_cmd = 'ooSubprocess: ' + ' '.join(cmd)
if verbose and out_fn and (not get_output):
print_stderr(print_cmd + ' > ' + out_fn)
elif verbose:
print_stderr(print_cmd)
if get_output:
result = subprocess.check_output(
cmd,
stdin=in_pipe,
**kwargs)
elif get_out_pipe:
tmp_file = NamedTemporaryFile(dir=self.tmp_dir)
p = subprocess.Popen(
cmd,
stdin=in_pipe,
stdout=tmp_file,
**kwargs)
p.wait()
if in_pipe != None:
in_pipe.close()
tmp_file.seek(0)
result = tmp_file
elif out_fn:
ofile = open(out_fn, 'w') if out_fn else None
result = subprocess.check_call(
cmd,
stdin=in_pipe,
stdout=ofile,
**kwargs)
ofile.close()
else:
result = subprocess.check_call(
cmd,
stdin=in_pipe,
**kwargs)
return result
def chain(
self,
prog,
args=[],
stop=False,
in_pipe=None,
get_output=False,
get_out_pipe=False,
out_fn=None,
verbose=True,
**kwargs):
if not which.is_exe(prog):
raise ooSubprocessException('Error: cannot find the program %s '\
'in the executable path!'%prog)
if in_pipe is None and self.chain_cmds != []:
raise ooSubprocessException(
'The pipeline was not stopped before creating a new one!'\
'In cache: %s' % (' | '.join(self.chain_cmds)))
if out_fn and stop == False:
raise ooSubprocessException(
'out_fn (output_file_name) is only specified when stop = True!')
if isinstance(args, str):
args = args.split()
if not isinstance(args, list):
args = [args]
cmd = [prog] + args
print_cmd = ' '.join(cmd)
if out_fn and (not get_output):
print_cmd += ' > ' + out_fn
self.chain_cmds.append(print_cmd)
if stop:
if in_pipe is None:
raise ooSubprocessException('No input process to create a pipeline!')
if verbose:
print_stderr('ooSubprocess: ' + ' | '.join(self.chain_cmds))
self.chain_cmds = []
if get_output:
result = subprocess.check_output(
cmd,
stdin=in_pipe,
**kwargs)
elif get_out_pipe:
tmp_file = NamedTemporaryFile(dir=self.tmp_dir)
p = subprocess.Popen(
cmd,
stdin=in_pipe,
stdout=tmp_file,
**kwargs)
return_code = p.wait()
if return_code != 0:
raise ooSubprocessException(
'Failed when executing the command: %s\n'\
'return code: %s'\
%(' | '.join(self.chain_cmds), return_code))
tmp_file.seek(0)
if in_pipe != None:
in_pipe.close()
result = tmp_file
elif out_fn:
ofile = open(out_fn, 'w')
result = subprocess.check_call(
cmd,
stdin=in_pipe,
stdout=ofile,
**kwargs)
ofile.close()
else:
result = subprocess.check_call(
cmd,
stdin=in_pipe,
**kwargs)
else:
tmp_file = NamedTemporaryFile(dir=self.tmp_dir)
p = subprocess.Popen(
cmd,
stdin=in_pipe,
stdout=tmp_file,
**kwargs)
return_code = p.wait()
if return_code != 0:
raise ooSubprocessException(
'Failed when executing the command: %s\n'\
'return code: %s'\
%(' | '.join(self.chain_cmds), return_code))
tmp_file.seek(0)
if in_pipe != None:
in_pipe.close()
result = tmp_file
return result
def ftmp(self, ifn):
return os.path.join(self.tmp_dir, os.path.basename(ifn))
def fdir(dir, ifn):
return os.path.join(dir, os.path.basename(ifn))
def mkdir(dir):
if not os.path.exists(dir):
try:
os.makedirs(dir)
except OSError as e:
if e.errno != 17:
raise
pass
elif not os.path.isdir(dir):
raise ooSubprocessException('Error: %s is not a directory!' % dir)
def replace_ext(ifn, old_ext, new_ext):
# if not os.path.isfile(ifn):
# print_stderr('Error: file %s does not exist!'%(ifn))
# exit(1)
if ifn[len(ifn) - len(old_ext):] != old_ext:
# print_stderr('Error: the old file extension %s does not match!'%old_ext)
# exit(1)
new_ifn = ifn + new_ext
else:
new_ifn = ifn[:len(ifn) - len(old_ext)] + new_ext
return new_ifn
def splitext(ifn):
basename = os.path.basename(ifn)
if ifn.endswith('.tar.bz2'):
ext = '.tar.bz2'
elif ifn.endswith('.tar.gz'):
ext = '.tar.gz'
else:
ext = basename.split('.')[-1]
if ext != basename:
ext = '.' + ext
base = basename[:-len(ext)]
for t in ['.sam', '.fastq', '.fasta', '.fna']:
if base.endswith(t):
ext = t + ext
base = base[:-len(t)]
return base, ext
def trace_unhandled_exceptions(f):
@functools.wraps(f)
def wrapper(*args, **kwargs):
try:
return f(*args, **kwargs)
except:
#traceback.print_exc()
#raise Exception(''.join(traceback.format_exception(*sys.exc_info())))
raise Exception(traceback.format_exc())
return wrapper
def parallelize(func, args, nprocs=1, use_threads=False):
if nprocs > 1:
if use_threads:
pool = ThreadPool(nprocs)
else:
pool = multiprocessing.Pool(nprocs)
results = pool.map(func, args)
pool.close()
pool.join()
else:
results = serialize(func, args)
return results
def parallelize_async(func, args, nprocs=1, use_threads=False):
if nprocs > 1:
if use_threads:
pool = ThreadPool(nprocs)
else:
pool = multiprocessing.Pool(nprocs)
app_results = []
for a in args:
app_results.append(pool.apply_async(func, [a]))
pool.close()
pool.join()
results = [r.get() for r in app_results]
else:
results = serialize(func, args)
return results
def serialize(func, args):
results = []
for arg in args:
results.append(func(arg))
return results
def print_stderr(*args):
sys.stderr.write(' '.join(map(str, args)) + '\n')
sys.stderr.flush()
def print_stdout(*args):
sys.stdout.write(' '.join(map(str, args)) + '\n')
sys.stdout.flush()
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