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annotate msconvert_wrapper.py @ 0:baa6c072fccc draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
author galaxyp
date Fri, 08 Apr 2016 16:08:09 -0400
parents
children 7016f1f10f42
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0
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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1 #!/usr/bin/env python
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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2 import optparse
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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3 import os
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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4 import sys
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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5 import tempfile
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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6 import shutil
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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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
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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16 tmp_stdout_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix='.stdout').name
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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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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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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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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 to_extensions = ['mzML', 'mzXML', 'unindexed_mzML', 'unindexed_mzXML', 'mgf', 'mz5', 'txt', 'ms2', 'cms2']
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92
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93
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94 def str_to_bool(v):
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95 """ From http://stackoverflow.com/questions/715417/converting-from-a-string-to-boolean-in-python """
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96 return v.lower() in ["yes", "true", "t", "1"]
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97
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98
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99 def _add_filter(filters_file, contents):
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100 filters_file.write("filter=%s\n" % contents)
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101
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102
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103 def _skip_line(options, file_num, line_parts):
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104 file_num_column = options.filter_table_file_column
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105 if not file_num_column:
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106 return False
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107 else:
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108 target_file_num_val = str(file_num).strip()
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109 query_file_num_val = line_parts[int(file_num_column) - 1].strip()
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110 #print "target %s, query %s" % (target_file_num_val, query_file_num_val)
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111 return target_file_num_val != query_file_num_val
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112
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113
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114 def _read_table_numbers(path, options, file_num=None):
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115 unique_numbers = set([])
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116 column_num = options.filter_table_column
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117 input = open(path, "r")
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118 first_line = True
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119 for line in input:
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120 if not line:
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121 continue
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122 line = line.strip()
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123 if line.startswith("#"):
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124 first_line = False
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125 continue
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126 if column_num == None:
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127 column = line
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128 else:
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129 line_parts = line.split("\t")
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130 if _skip_line(options, file_num, line_parts):
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131 continue
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132 column = line_parts[int(column_num) - 1]
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133 match = re.match("\d+", column)
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134 if match:
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135 unique_numbers.add(int(match.group()))
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136 first_line = False
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137 return unique_numbers
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138
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139
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140 def shellquote(s):
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141 return '"' + s.replace('"', '\\"') + '"'
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142
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143
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144 def _add_filter_line_from_file(filter_file, options, file_num=None):
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145 file = options.filter_table
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146 if not file:
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147 return
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148 numbers = _read_table_numbers(file, options, file_num)
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149 msconvert_int_set = " ".join([str(number) for number in numbers])
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150 filter_type = options.filter_table_type
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151 if filter_type == 'number':
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152 filter_prefix = 'scanNumber'
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153 else:
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154 filter_prefix = 'index'
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155 _add_filter(filter_file, "%s %s" % (filter_prefix, msconvert_int_set))
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156
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157
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158 def _create_filters_file(options, file_num=None, debug=False):
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159 suffix = "" if not file_num else str(file_num)
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160 filters_file_path = "filters%s" % suffix
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161 filters_file = open(filters_file_path, "w")
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162 if options.filters_file:
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163 filters_file.write(open(options.filters_file, "r").read())
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164 for filter in options.filter:
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165 _add_filter(filters_file, filter)
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166 _add_filter_line_from_file(filters_file, options, file_num=file_num)
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167
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168 filters_file.close()
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169 if debug:
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170 print(( open(filters_file_path, "r").read() ))
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171 return filters_file_path
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172
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173
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174 def _build_base_cmd(options,args=None):
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175 to_extension = options.toextension
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176 if to_extension.startswith("unindexed_"):
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177 to_extension = to_extension[len("unindexed_"):]
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178 to_params = "--noindex"
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179 else:
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180 to_params = ""
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181 cmd = "msconvert --%s %s" % (to_extension, to_params)
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182 if args:
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183 cmd = "%s %s" % (cmd, ' '.join(args))
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184 if str_to_bool(options.zlib):
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185 cmd = "%s %s" % (cmd, "--zlib")
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186 if options.binaryencoding:
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187 cmd = "%s --%s" % (cmd, options.binaryencoding)
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188 if options.mzencoding:
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189 cmd = "%s --mz%s" % (cmd, options.mzencoding)
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190 if options.intensityencoding:
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191 cmd = "%s --inten%s" % (cmd, options.intensityencoding)
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192 return cmd
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193
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194
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195 def _run(base_cmd, output_dir='output', inputs=[], debug=False):
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196 inputs_as_str = " ".join(['%s' % shellquote(input) for input in inputs])
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197 os.mkdir(output_dir)
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198 cmd = "%s -o %s %s" % (base_cmd, shellquote(output_dir), inputs_as_str)
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199 if debug:
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200 print(cmd)
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201 execute(cmd)
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202 output_files = os.listdir(output_dir)
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203 assert len(output_files) == 1
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204 output_file = output_files[0]
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205 return os.path.join(output_dir, output_file)
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206
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207
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208 def run_script():
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209 parser = optparse.OptionParser()
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210 parser.add_option('--input', dest='inputs', action='append', default=[])
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211 parser.add_option('--input_name', dest='input_names', action='append', default=[])
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212 parser.add_option('--implicit', dest='implicits', action='append', default=[], help='input files that should NOT be on the msconvert command line.')
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213 parser.add_option('--ident', dest='idents', action='append', default=[])
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214 parser.add_option('--ident_name', dest='ident_names', action='append', default=[])
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215 parser.add_option('--output', dest='output')
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216 parser.add_option('--refinement', dest='refinement')
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217 parser.add_option('--fromextension', dest='fromextension')
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218 parser.add_option('--toextension', dest='toextension', default='mzML', choices=to_extensions)
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219 parser.add_option('--binaryencoding', dest='binaryencoding', choices=['32', '64'])
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220 parser.add_option('--mzencoding', dest='mzencoding', choices=['32', '64'])
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221 parser.add_option('--intensityencoding', dest='intensityencoding', choices=['32', '64'])
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222 parser.add_option('--zlib', dest='zlib', default="false")
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223 parser.add_option('--filter', dest='filter', action='append', default=[])
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224 parser.add_option('--filters_file', dest='filters_file', default=None)
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225 parser.add_option('--filter_table', default=None)
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226 parser.add_option('--filter_table_type', default='index', choices=['index', 'number'])
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227 parser.add_option('--filter_table_column', default=None)
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228 parser.add_option('--filter_table_file_column', default=None)
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229 parser.add_option('--debug', dest='debug', action='store_true', default=False)
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230
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231 (options, args) = parser.parse_args()
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232 if len(options.inputs) < 1:
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233 stop_err("No input files to msconvert specified")
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234 if len(options.input_names) > 0 and len(options.input_names) != len(options.inputs):
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235 stop_err("Number(s) of supplied input names and input files do not match")
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236 if not options.output:
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237 stop_err("Must specify output location")
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238 input_files = []
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239 for i, input in enumerate(options.inputs):
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240 input_base = None
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241 if len(options.input_names) > i:
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242 input_base = options.input_names[i]
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243 input_base = input_base.replace("'", "").replace("\"", "")
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244 print("1- input_base: %s" % input_base)
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245 if not input_base:
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246 input_base = 'input%s' % i
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247 print("2- input_base: %s" % input_base)
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248 if not input_base.lower().endswith('.%s' % options.fromextension.lower()) and input not in options.implicits:
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249 input_file = '%s.%s' % (input_base, options.fromextension)
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250 print("3- input_base: %s" % input_base)
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251 print("3- input_file: %s" % input_file)
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252 else:
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253 input_file = input_base
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254 print("4- input_base: %s" % input_base)
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255 print("4- input_file: %s" % input_file)
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256 input_file = input_file
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257 copy_to_working_directory(input, input_file)
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258 if input in options.implicits:
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259 continue
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260 input_files.append(input_file)
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261 for i, ident in enumerate(options.idents):
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262 ident_file = options.ident_names[i]
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263 copy_to_working_directory(ident, ident_file)
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264
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265 cmd = _build_base_cmd(options,args=args)
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266 file_column = options.filter_table_file_column
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267 if not file_column:
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268 # Apply same filters to all files, just create a unviersal filter files
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269 # and run msconvert once.
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270 filters_file_path = _create_filters_file(options, debug=options.debug)
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271 cmd = "%s -c %s" % (cmd, filters_file_path)
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272 else:
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273 # Dispatching on a column to filter different files differently, need to filter
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274 # each input once with msconvert and then merge once.
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275 filtered_files = []
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276 for index, input_file in enumerate(input_files):
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277 filters_file_path = _create_filters_file(options, index + 1, debug=options.debug)
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278 filter_cmd = "%s -c %s" % (cmd, filters_file_path)
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279 filtered_output_file = _run(filter_cmd, output_dir='output%d' % index, inputs=[input_file], debug=options.debug)
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280 filtered_files.append(filtered_output_file)
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281 input_files = filtered_files
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282 if len(input_files) > 1:
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283 cmd = "%s --merge" % cmd
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284 output_file = _run(cmd, output_dir='output', inputs=input_files, debug=options.debug)
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285 shutil.copy(output_file, options.output)
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286 if options.refinement:
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287 # .mzRefinement.tsv
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288 files = os.listdir(os.getcwd())
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289 for fname in files:
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290 if fname.endswith('.mzRefinement.tsv'):
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291 shutil.copy(fname, options.refinement)
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292 break
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293
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294 def __main__():
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295 run_script()
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296
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297 if __name__ == '__main__':
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298 __main__()