Mercurial > repos > miller-lab > genome_diversity
view gd_util.py @ 36:51cd0307fb70
Phylip's extra ouputs are now stored in the job working directory
author | Richard Burhans <burhans@bx.psu.edu> |
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date | Wed, 20 Nov 2013 16:32:01 -0500 |
parents | 8997f2ca8c7a |
children |
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#!/usr/bin/env python import base64 import errno import os import subprocess import sys import zlib ################################################################################ def die(message): print >> sys.stderr, message sys.exit(1) ################################################################################ def mkdir_p(path): try: os.makedirs(path) except OSError, e: if e.errno <> errno.EEXIST: raise ################################################################################ def run_program(prog, args, stdout=subprocess.PIPE, stderr=subprocess.PIPE): kwargs = { "bufsize": -1, "close_fds": False, "creationflags": 0, "cwd": None, "env": None, "executable": prog, "preexec_fn": None, "shell": False, "startupinfo": None, "stderr": stderr, "stdin": None, "stdout": stdout, "universal_newlines": False } str_args = [str(x) for x in args] p = subprocess.Popen(str_args, **kwargs) (stdoutdata, stderrdata) = p.communicate() rc = p.returncode if rc != 0: die('FAILED:\n{0}\nCOMMAND:\n{1}'.format(stderrdata, ' '.join(str_args))) return stdoutdata, stderrdata ################################################################################ def unwrap_string(string): try: decoded_string = base64.b64decode(string) except TypeError, message: die('base64.b64decode: {0}: {1}'.format(message, string)) try: return zlib.decompress(decoded_string) except zlib.error, message: die('zlib.decompress: {0}'.format(message)) ################################################################################ def wrap_string(string, level=9): try: compressed_string = zlib.compress(string, level) except zlib.error, message: die('zlib.compress: {0}'.format(message)) return base64.b64encode(compressed_string) ################################################################################