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1 #!/usr/bin/env python
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2
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3 """
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4 Author: George Weingart
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5 Description: Wrapper program for maaslin
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6 """
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7
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8 #####################################################################################
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9 #Copyright (C) <2012>
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10 #
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11 #Permission is hereby granted, free of charge, to any person obtaining a copy of
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12 #this software and associated documentation files (the "Software"), to deal in the
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13 #Software without restriction, including without limitation the rights to use, copy,
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14 #modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
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15 #and to permit persons to whom the Software is furnished to do so, subject to
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16 #the following conditions:
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17 #
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18 #The above copyright notice and this permission notice shall be included in all copies
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19 #or substantial portions of the Software.
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20 #
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21 #THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
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22 #INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
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23 #PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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24 #HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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25 #OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
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26 #SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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27 #####################################################################################
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28
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29 __author__ = "George Weingart"
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30 __copyright__ = "Copyright 2012"
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31 __credits__ = ["George Weingart"]
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32 __license__ = "MIT"
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33 __maintainer__ = "George Weingart"
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34 __email__ = "george.weingart@gmail.com"
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35 __status__ = "Development"
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36
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37 from cStringIO import StringIO
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38 import sys,string
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39 import os
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40 import tempfile
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41 from pprint import pprint
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42 import argparse
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43
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44 ######################################################################################
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45 # Parse input parms #
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46 ######################################################################################
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47 def read_params(x):
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48 parser = argparse.ArgumentParser(description='MaAsLin Argparser')
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49 parser.add_argument('--lastmeta', action="store", dest='lastmeta',nargs='?')
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50 parser.add_argument('--input', action="store", dest='input',nargs='?')
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51 parser.add_argument('--output', action="store", dest='output',nargs='?')
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52 parser.add_argument('--zip_file', action="store", dest='zip_file',nargs='?')
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53 parser.add_argument('--alpha', action="store", type=float,default=0.05,dest='alpha',nargs='?')
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54 parser.add_argument('--min_abd', action="store", type=float,default=0.0001,dest='min_abd',nargs='?')
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55 parser.add_argument('--min_samp', action="store", type=float,default=0.01,dest='min_samp',nargs='?')
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56 parser.add_argument('--tool_option1', action="store", dest='tool_option1',nargs='?')
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57 return parser
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58
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59
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60
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61 ######################################################################################
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62 # Build read config file #
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63 ######################################################################################
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64 def build_read_config_file(strTempDir,results, DSrc, DMaaslin, root_dir):
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65 fname = results.input
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66 input_file = open(fname)
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67 input_lines = input_file.readlines()
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68 LenInput = len(input_lines)
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69 input_file.close()
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70 TopLimit = int(results.lastmeta)
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71 ReadConfigFileName = os.path.join(strTempDir,"Test.read.config")
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72 Q = "'"
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73
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74 #WorkingDir = os.getcwd()
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75 WorkingDir = root_dir
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76 os.chdir(DMaaslin)
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77
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78 Limit1 = Q + "2-" + str(TopLimit ) + Q
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79 ReadConfigTb1 = [
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80 os.path.join(DSrc,"CreateReadConfigFile.R"),
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81 "-c",
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82 Limit1,
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83 ReadConfigFileName,
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84 "Metadata"
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85 ">/dev/null",\
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86 "2>&1"
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87 ]
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88
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89 cmd_config1 = " ".join(ReadConfigTb1)
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90
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91 os.system(cmd_config1)
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92
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93 Limit2 = Q + str(TopLimit +1 ) + '-' + Q
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94 ReadConfigTb2 = [
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95 os.path.join(DSrc,"CreateReadConfigFile.R"),
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96 "-a",
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97 "-c",
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98 Limit2,
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99 ReadConfigFileName,
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100 "Abundance"
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101 ">/dev/null",\
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102 "2>&1"
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103 ]
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104
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105 cmd_config2 = " ".join(ReadConfigTb2)
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106 os.system(cmd_config2)
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107 os.chdir(WorkingDir)
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108 return ReadConfigFileName
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109
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110
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111 ######################################################################################
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112 # Main Program #
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113 ######################################################################################
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114
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115 # Parse commandline in
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116 parser = read_params( sys.argv )
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117 results = parser.parse_args()
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118 root_dir = os.environ.get('maaslin_SCRIPT_PATH')
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119
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120
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121
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122
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123
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124
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125 ### If option 2 is selected inform user on 2 outputs
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126 if results.tool_option1 == "2":
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127 print "***Please note: 2 output files are generated: Complete zipped results + Summary ***"
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128
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129 ### Project name
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130 strProjectName = os.path.splitext(os.path.basename(results.input))[0]
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131
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132 ### Define directory locations
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133 D = os.path.join(root_dir)
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134 DSrc = os.path.join(root_dir,"src")
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135 DInput = os.path.join(root_dir,"maaslin","input")
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136 DMaaslin = os.path.join(root_dir)
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137
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138 DMaaslinGalaxy = os.path.join(root_dir)
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139
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140
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141
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142 ### Make temporary folder to work in
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143 ### Change permissions to make useable
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144 strTempDir = tempfile.mkdtemp()
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145 cmd_chmod = "chmod 755 /" + strTempDir
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146 os.system(cmd_chmod)
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147 cmd_mkdir1 = "mkdir -m 755 " + os.path.join(strTempDir,strProjectName)
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148 os.system(cmd_mkdir1)
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149
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150 ### Transpose the pcl file to a tsv file
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151 TbCmdTranspose = [\
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152 "python",
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153 DMaaslinGalaxy + "/transpose.py<" + str(results.input) + ">" + os.path.join(strTempDir,"output.tsv")\
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154 ]
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155 cmd_transpose = " ".join(TbCmdTranspose)
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156 os.system(cmd_transpose)
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157
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158 ### Make path for target output file
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159 OutputFile = os.path.join(strTempDir,strProjectName,strProjectName+".txt")
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160
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161 ### Make read config file
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162 ReadConfigFileName = build_read_config_file(strTempDir,results, DSrc, DMaaslin, root_dir)
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163
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164 ### Build MaAsLin comamnd
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165 CmdsArray = [\
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166 os.path.join(DSrc,"Maaslin.R"), \
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167 "-d", str(results.alpha),\
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168 "-r", str(results.min_abd),\
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169 "-p", str(results.min_samp), \
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170 "-i", \
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171 ReadConfigFileName, \
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172 OutputFile, \
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173 os.path.join(strTempDir,"output.tsv"), \
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174 "-v",\
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175 "ERROR",\
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176 ">/dev/null",\
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177 "2>&1"
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178 ]
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179
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180 invoke_maaslin_cmd = " ".join(CmdsArray)
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181
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182
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183
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184
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185
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186 ### Write to directory cmd line used for troubleshooting
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187 #CmdFileName = os.path.join(strTempDir,"cmdfile.txt")
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188 #OutFile = open(CmdFileName,"w")
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189 #OutputString = invoke_maaslin_cmd + "\n"
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190 #OutFile.write(OutputString)
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191 #OutFile.close()
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192
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193 ### Call MaAsLin
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194 os.system(invoke_maaslin_cmd)
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195
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196
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197 ### Copy output file to make available to galaxy
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198 cmd_copy = "cp " + os.path.join(strTempDir,strProjectName+"/output.txt") + " " + results.output
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199 MsgFileName = os.path.join(strTempDir,strProjectName+"/output.txt")
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200
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201 if not os.path.isfile(MsgFileName):
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202 cmd_copy = "cp " + os.path.join(strTempDir,strProjectName+"/output.txt") + " " + results.output
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203 OutFile = open(MsgFileName,"w")
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204 OutputString = "A MaAsLin error has occurred\n"
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205 OutputString = OutputString + "It typically happens when incorrect 'Last metadata row' was selected\n"
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206 OutputString = OutputString + "For demo data please choose 'Weight'\n"
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207 OutFile.write(OutputString)
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208 OutFile.close()
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209
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210 os.system(cmd_copy)
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211
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212 ### Zip up output folder
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213 cmd_zip = "zip -jr " + os.path.join(strTempDir,strProjectName+".zip") + " " + os.path.join(strTempDir,strProjectName) + ">/dev/null 2>&1"
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214
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215 os.system(cmd_zip)
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216
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217 ### Copy output folder to make available to galaxy
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218 cmd_copy_zip = "cp " + os.path.join(strTempDir,strProjectName+".zip") + " " + results.zip_file
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219 os.system(cmd_copy_zip)
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220
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221 ### Delete temp directory
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222 cmd_del_tempdir = "rm -r " + strTempDir
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223 ######os.system(cmd_del_tempdir)
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