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1 #!/usr/bin/env python
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2 import optparse
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3 import os
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4 import sys
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5 import tempfile
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6 import shutil
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7 import subprocess
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8 import re
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9 from os.path import basename
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10 import logging
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11
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12 assert sys.version_info[:2] >= ( 2, 6 )
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13
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14 log = logging.getLogger(__name__)
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15 working_directory = os.getcwd()
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16 tmp_stderr_name = tempfile.NamedTemporaryFile(dir = working_directory, suffix = '.stderr').name
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17 tmp_stdout_name = tempfile.NamedTemporaryFile(dir = working_directory, suffix = '.stdout').name
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18
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19 def stop_err( msg ):
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20 sys.stderr.write( "%s\n" % msg )
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21 sys.exit()
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22
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23 def read_stderr():
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24 stderr = ''
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25 if(os.path.exists(tmp_stderr_name)):
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26 with open(tmp_stderr_name, 'rb') as tmp_stderr:
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27 buffsize = 1048576
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28 try:
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29 while True:
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30 stderr += tmp_stderr.read(buffsize)
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31 if not stderr or len(stderr) % buffsize != 0:
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32 break
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33 except OverflowError:
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34 pass
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35 return stderr
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36
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37 def execute(command, stdin=None):
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38 with open(tmp_stderr_name, 'wb') as tmp_stderr:
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39 with open(tmp_stdout_name, 'wb') as tmp_stdout:
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40 proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)
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41 returncode = proc.wait()
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42 if returncode != 0:
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43 raise Exception, "Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr())
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44
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45 def delete_file(path):
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46 if os.path.exists(path):
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47 try:
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48 os.remove(path)
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49 except:
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50 pass
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51
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52 def delete_directory(directory):
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53 if os.path.exists(directory):
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54 try:
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55 shutil.rmtree(directory)
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56 except:
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57 pass
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58
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59 def symlink(source, link_name):
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60 import platform
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61 if platform.system() == 'Windows':
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62 import win32file
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63 win32file.CreateSymbolicLink(source, link_name, 1)
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64 else:
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65 os.symlink(source, link_name)
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66
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67
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68 def copy_to_working_directory(data_file, relative_path):
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69 if os.path.abspath(data_file) != os.path.abspath(relative_path):
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70 shutil.copy(data_file, relative_path)
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71 return relative_path
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72
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73 def __main__():
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74 run_script()
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75
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76 #ENDTEMPLATE
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77
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78 to_extensions = ['mzML', 'mzXML', 'mgf', 'txt', 'ms2', 'cms2']
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79
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80 def str_to_bool(v):
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81 """ From http://stackoverflow.com/questions/715417/converting-from-a-string-to-boolean-in-python """
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82 return v.lower() in ["yes", "true", "t", "1"]
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83
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84
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85 def run_script():
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86 parser = optparse.OptionParser()
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87 parser.add_option('--input', dest='input')
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88 parser.add_option('--output', dest='output')
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89 parser.add_option('--fromextension', dest='fromextension')
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90 parser.add_option('--toextension', dest='toextension', default='mzML', choices=to_extensions)
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91 parser.add_option('--binaryencoding', dest='binaryencoding', choices=['32', '64'])
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92 parser.add_option('--mzencoding', dest='mzencoding', choices=['32', '64'])
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93 parser.add_option('--intensityencoding', dest='intensityencoding', choices=['32', '64'])
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94 parser.add_option('--noindex', dest='noindex')
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95 parser.add_option('--zlib', dest='zlib')
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96 parser.add_option('--filter', dest='filter', action='append', default=[])
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97
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98 (options, args) = parser.parse_args()
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99
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100 filter_commands = ''
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101 for filter in options.filter:
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102 filter_commands = "%s --filter \"%s\"" % (filter_commands, filter)
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103
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104 input_file = 'input.%s' % options.fromextension
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105 copy_to_working_directory(options.input, input_file)
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106 os.mkdir('output')
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107 cmd = "msconvert --%s -o output" % (options.toextension)
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108 if str_to_bool(options.noindex):
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109 cmd = "%s %s" % (cmd, "--noindex")
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110 if str_to_bool(options.zlib):
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111 cmd = "%s %s" % (cmd, "--zlib")
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112 cmd = "%s --%s" % (cmd, options.binaryencoding)
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113 cmd = "%s --mz%s" % (cmd, options.mzencoding)
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114 cmd = "%s --inten%s" % (cmd, options.intensityencoding)
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115 cmd = "%s %s" % (cmd, input_file)
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116 cmd = "%s %s" % (cmd, filter_commands)
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117 print cmd
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118 execute(cmd)
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119 output_files = os.listdir('output')
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120 assert len(output_files) == 1
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121 output_file = output_files[0]
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122 shutil.copy(os.path.join('output', output_file), options.output)
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123
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124 if __name__ == '__main__': __main__()
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