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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 try:
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39 with open(tmp_stderr_name, 'wb') as tmp_stderr:
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40 with open(tmp_stdout_name, 'wb') as tmp_stdout:
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41 proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)
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42 returncode = proc.wait()
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43 if returncode != 0:
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44 raise Exception, "Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr())
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45 finally:
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46 print open(tmp_stderr_name, "r").read()
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47 print open(tmp_stdout_name, "r").read()
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48
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49
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50 def delete_file(path):
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51 if os.path.exists(path):
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52 try:
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53 os.remove(path)
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54 except:
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55 pass
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56
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57 def delete_directory(directory):
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58 if os.path.exists(directory):
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59 try:
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60 shutil.rmtree(directory)
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61 except:
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62 pass
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63
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64 def symlink(source, link_name):
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65 import platform
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66 if platform.system() == 'Windows':
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67 import win32file
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68 win32file.CreateSymbolicLink(source, link_name, 1)
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69 else:
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70 os.symlink(source, link_name)
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71
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72
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73 def copy_to_working_directory(data_file, relative_path):
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74 if os.path.abspath(data_file) != os.path.abspath(relative_path):
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75 shutil.copy(data_file, relative_path)
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76 return relative_path
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77
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78 def __main__():
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79 run_script()
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80
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81 #ENDTEMPLATE
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82
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83 to_extensions = ['mzML', 'mzXML', 'unindexed_mzML', 'unindexed_mzXML', 'mgf', 'txt', 'ms2', 'cms2']
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84
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85
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86 def str_to_bool(v):
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87 """ From http://stackoverflow.com/questions/715417/converting-from-a-string-to-boolean-in-python """
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88 return v.lower() in ["yes", "true", "t", "1"]
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89
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90
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91 def _add_filter(filters_file, contents):
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92 filters_file.write("filter=\"%s\"\n" % contents)
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93
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94
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95 def _read_table_numbers(path):
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96 unique_numbers = set([])
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97 input = open(path, "r")
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98 first_line = True
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99 for line in input:
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100 if not line:
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101 continue
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102 line = line.strip()
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103 if line.startswith("#"):
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104 first_line = False
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105 continue
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106 match = re.match("\d+", line)
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107 if match:
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108 unique_numbers.add(int(match.group()))
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109 first_line = False
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110 return unique_numbers
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111
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112
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113 def _add_filter_line_from_file(file, filter_file, filter_prefix):
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114 if not file:
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115 return
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116 numbers = _read_table_numbers(file)
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117 msconvert_int_set = " ".join([str(number) for number in numbers])
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118 _add_filter(filter_file, "%s %s" % (filter_prefix, msconvert_int_set))
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119
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120
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121 def _create_filters_file(options):
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122 filters_file_path = "filters"
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123 filters_file = open(filters_file_path, "w")
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124 if options.filters_file:
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125 filters_file.write(open(options.filters_file, "r").read())
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126 for filter in options.filter:
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127 _add_filter(filters_file, filter)
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128 _add_filter_line_from_file(options.filter_indices_table, filters_file, "index")
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129 _add_filter_line_from_file(options.filter_numbers_table, filters_file, "scanNumber")
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130
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131 filters_file.close()
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132 print open(filters_file_path, "r").read()
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133 return filters_file_path
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134
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135
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136 def run_script():
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137 parser = optparse.OptionParser()
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138 parser.add_option('--input', dest='input')
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139 parser.add_option('--output', dest='output')
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140 parser.add_option('--fromextension', dest='fromextension')
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141 parser.add_option('--toextension', dest='toextension', default='mzML', choices=to_extensions)
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142 parser.add_option('--binaryencoding', dest='binaryencoding', choices=['32', '64'])
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143 parser.add_option('--mzencoding', dest='mzencoding', choices=['32', '64'])
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144 parser.add_option('--intensityencoding', dest='intensityencoding', choices=['32', '64'])
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145 parser.add_option('--zlib', dest='zlib', default="false")
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146 parser.add_option('--filter', dest='filter', action='append', default=[])
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147 parser.add_option('--filters_file', dest='filters_file', default=None)
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148 parser.add_option('--filter_indices_table', default=None)
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149 parser.add_option('--filter_numbers_table', default=None)
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150
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151 (options, args) = parser.parse_args()
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152
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153 input_file = 'input.%s' % options.fromextension
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154 copy_to_working_directory(options.input, input_file)
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155 os.mkdir('output')
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156 to_extension = options.toextension
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157 if to_extension.startswith("unindexed_"):
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158 to_extension = to_extension[len("unindexed_"):]
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159 to_params = "--noindex"
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160 else:
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161 to_params = ""
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162 cmd = "msconvert --%s %s -o output" % (to_extension, to_params)
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163 if str_to_bool(options.zlib):
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164 cmd = "%s %s" % (cmd, "--zlib")
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165 if options.binaryencoding:
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166 cmd = "%s --%s" % (cmd, options.binaryencoding)
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167 if options.mzencoding:
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168 cmd = "%s --mz%s" % (cmd, options.mzencoding)
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169 if options.intensityencoding:
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170 cmd = "%s --inten%s" % (cmd, options.intensityencoding)
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171 cmd = "%s %s" % (cmd, input_file)
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172 filters_file_path = _create_filters_file(options)
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173 cmd = "%s -c %s" % (cmd, filters_file_path)
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174 print cmd
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175 execute(cmd)
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176 output_files = os.listdir('output')
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177 assert len(output_files) == 1
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178 output_file = output_files[0]
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179 shutil.copy(os.path.join('output', output_file), options.output)
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180
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181
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182 if __name__ == '__main__': __main__()
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