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annotate gd_util.py @ 27:8997f2ca8c7a

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Update to Miller Lab devshed revision bae0d3306d3b
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 15 Jul 2013 10:47:35 -0400
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27
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1 #!/usr/bin/env python
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2
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3 import base64
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4 import errno
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5 import os
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6 import subprocess
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7 import sys
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8 import zlib
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9
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10 ################################################################################
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11
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12 def die(message):
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13 print >> sys.stderr, message
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14 sys.exit(1)
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15
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16 ################################################################################
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17
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18 def mkdir_p(path):
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19 try:
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20 os.makedirs(path)
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21 except OSError, e:
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22 if e.errno <> errno.EEXIST:
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23 raise
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24
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25 ################################################################################
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26
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27 def run_program(prog, args, stdout=subprocess.PIPE, stderr=subprocess.PIPE):
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28 kwargs = {
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29 "bufsize": -1,
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30 "close_fds": False,
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31 "creationflags": 0,
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32 "cwd": None,
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33 "env": None,
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34 "executable": prog,
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35 "preexec_fn": None,
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36 "shell": False,
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37 "startupinfo": None,
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38 "stderr": stderr,
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39 "stdin": None,
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40 "stdout": stdout,
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41 "universal_newlines": False
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42 }
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43
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44 str_args = [str(x) for x in args]
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45
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46 p = subprocess.Popen(str_args, **kwargs)
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47 (stdoutdata, stderrdata) = p.communicate()
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48 rc = p.returncode
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49
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50 if rc != 0:
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51 die('FAILED:\n{0}\nCOMMAND:\n{1}'.format(stderrdata, ' '.join(str_args)))
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52
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53 return stdoutdata, stderrdata
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54
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55 ################################################################################
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56
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57 def unwrap_string(string):
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58 try:
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59 decoded_string = base64.b64decode(string)
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60 except TypeError, message:
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61 die('base64.b64decode: {0}: {1}'.format(message, string))
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62
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63 try:
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64 return zlib.decompress(decoded_string)
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65 except zlib.error, message:
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66 die('zlib.decompress: {0}'.format(message))
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67
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68 ################################################################################
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69
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70 def wrap_string(string, level=9):
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71 try:
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72 compressed_string = zlib.compress(string, level)
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73 except zlib.error, message:
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74 die('zlib.compress: {0}'.format(message))
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75 return base64.b64encode(compressed_string)
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76
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77 ################################################################################