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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 import logging
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10
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11 assert sys.version_info[:2] >= (2, 6)
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12
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13 log = logging.getLogger(__name__)
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14 working_directory = os.getcwd()
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15 tmp_stderr_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix='.stderr').name
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16 tmp_stdout_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix='.stdout').name
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17
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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
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24 def read_stderr():
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25 stderr = ''
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26 if(os.path.exists(tmp_stderr_name)):
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27 with open(tmp_stderr_name, 'rb') as tmp_stderr:
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28 buffsize = 1048576
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29 try:
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30 while True:
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31 stderr += tmp_stderr.read(buffsize)
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32 if not stderr or len(stderr) % buffsize != 0:
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33 break
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34 except OverflowError:
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35 pass
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36 return stderr
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37
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38
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39 def execute(command, stdin=None):
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40 try:
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41 with open(tmp_stderr_name, 'wb') as tmp_stderr:
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42 with open(tmp_stdout_name, 'wb') as tmp_stdout:
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43 proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)
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44 returncode = proc.wait()
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45 if returncode != 0:
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46 raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))
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47 finally:
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48 print(( open(tmp_stderr_name, "r").read() ))
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49 print(( open(tmp_stdout_name, "r").read() ))
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50
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51
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52 def delete_file(path):
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53 if os.path.exists(path):
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54 try:
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55 os.remove(path)
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56 except:
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57 pass
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58
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59
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60 def delete_directory(directory):
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61 if os.path.exists(directory):
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62 try:
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63 shutil.rmtree(directory)
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64 except:
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65 pass
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66
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67
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68 def symlink(source, link_name):
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69 import platform
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70 if platform.system() == 'Windows':
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71 try:
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72 import win32file
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73 win32file.CreateSymbolicLink(source, link_name, 1)
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74 except:
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75 shutil.copy(source, link_name)
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76 else:
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77 os.symlink(source, link_name)
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78
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79
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80 def copy_to_working_directory(data_file, relative_path):
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81 if os.path.abspath(data_file) != os.path.abspath(relative_path):
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82 symlink(data_file, relative_path)
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83 return relative_path
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84
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85
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86 def __main__():
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87 run_script()
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88
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89 #ENDTEMPLATE
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90
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91 def str_to_bool(v):
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92 """ From http://stackoverflow.com/questions/715417/converting-from-a-string-to-boolean-in-python """
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93 return v.lower() in ["yes", "true", "t", "1"]
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94
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95 def shellquote(s):
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96 return '"' + s.replace('"', '\\"') + '"'
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97
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98 def run_script():
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99 parser = optparse.OptionParser()
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100 parser.add_option('--input', dest='inputs', action='append', default=[])
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101 parser.add_option('--input_name', dest='input_names', action='append', default=[])
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102 parser.add_option('--implicit', dest='implicits', action='append', default=[], help='input files that should NOT be on the AB SCIEX MS Data Converter command line.')
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103 parser.add_option('--output', dest='output')
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104 parser.add_option('--fromextension', dest='fromextension')
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105 parser.add_option('--toextension', dest='toextension', default='mzML', choices=['mzML', 'mgf'])
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106 parser.add_option('--content_type', dest='content_type', default='centroid', choices=['profile', 'centroid', 'proteinpilot'])
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107 parser.add_option('--binaryencoding', dest='binaryencoding', choices=['32', '64'])
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108 parser.add_option('--zlib', dest='zlib', default="false")
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109 parser.add_option('--index', dest='index', default="false")
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110 parser.add_option('--debug', dest='debug', action='store_true', default=False)
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111
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112 (options, args) = parser.parse_args()
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113 if len(options.inputs) < 1:
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114 stop_err("No input files to ms_data_convert specified")
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115 if len(options.input_names) > 0 and len(options.input_names) != len(options.inputs):
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116 stop_err("Number(s) of supplied input names and input files do not match")
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117 if not options.output:
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118 stop_err("Must specify output location")
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119 input_files = []
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120 for i, input in enumerate(options.inputs):
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121 input_base = None
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122 if len(options.input_names) > i:
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123 input_base = options.input_names[i]
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124 input_base = input_base.replace("'", "").replace("\"", "")
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125 print("1- input_base: %s" % input_base)
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126 if not input_base:
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127 input_base = 'input%s' % i
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128 print("2- input_base: %s" % input_base)
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129 if not input_base.lower().endswith(options.fromextension.lower()) and input not in options.implicits:
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130 input_file = '%s.%s' % (input_base, options.fromextension)
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131 print("3- input_base: %s" % input_base)
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132 print("3- input_file: %s" % input_file)
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133 else:
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134 input_file = input_base
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135 print("4- input_base: %s" % input_base)
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136 print("4- input_file: %s" % input_file)
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137 input_file = input_file
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138 copy_to_working_directory(input, input_file)
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139 if input not in options.implicits:
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140 input_files.append(input_file)
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141 ## AB_SCIEX_MS_Converter <input format> <input data> <output content type> <output format> <output file> [data compression setting] [data precision setting] [create index flag]
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142 inputs_as_str = " ".join(['%s' % shellquote(input) for input in input_files])
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143 output_file = re.sub('(%s)?$' % options.fromextension.lower(), options.toextension, input_files[0].lower())
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144 cmd = "AB_SCIEX_MS_Converter %s %s %s %s %s" % (options.fromextension.upper(), inputs_as_str, options.content_type, options.toextension.upper(), output_file )
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145 if str_to_bool(options.zlib):
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146 cmd = "%s %s" % (cmd, "/zlib")
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147 if options.binaryencoding:
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148 cmd = "%s %s" % (cmd, "/singleprecision" if options.binaryencoding == '32' else "/doubleprecision")
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149 if str_to_bool(options.zlib):
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150 cmd = "%s %s" % (cmd, "/index")
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151 if options.debug:
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152 print(cmd)
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153 execute(cmd)
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154 shutil.copy(output_file, options.output)
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155
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156 if __name__ == '__main__':
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157 __main__()
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