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1 #abims_sartools_edger_wrapper.py
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2 #Author: Loraine Gueguen
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3 # imports
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4 import os, argparse
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5
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6
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7
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8 def main():
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9
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10 print("Start of galaxy wrapper")
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11
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12 #Check R and Rscript are installed
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13 check_r_cmd="command -v R >/dev/null 2>&1 || { echo >&2 'This tool requires R but it is not installed. Aborting.'; exit 1; }"
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14 check_rscript_cmd="command -v Rscript >/dev/null 2>&1 || { echo >&2 'This tool requires Rscript but it is not installed. Aborting.'; exit 1; }"
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15 os.system(check_r_cmd)
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16 os.system(check_rscript_cmd)
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17
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18 #Get arguments
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19 parser = argparse.ArgumentParser()
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20 parser.add_argument('--projectName')
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21 parser.add_argument('--author')
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22 parser.add_argument('--targetFile')
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23 parser.add_argument('--rawDir')
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24 parser.add_argument('--featuresToRemove')
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25 parser.add_argument('--varInt')
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26 parser.add_argument('--condRef')
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27 parser.add_argument('--batch')
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28 parser.add_argument('--alpha')
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29 parser.add_argument('--pAdjustMethod')
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30 parser.add_argument('--cpmCutoff')
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31 parser.add_argument('--geneSelection')
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32 parser.add_argument('--normalizationMethod')
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33 parser.add_argument('--colors')
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3
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34 parser.add_argument('--forceCairoGraph')
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0
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35 parser.add_argument('--figures_html')
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36 parser.add_argument('--figures_html_files_path')
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37 parser.add_argument('--tables_html')
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38 parser.add_argument('--tables_html_files_path')
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39 parser.add_argument('--rdata')
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40 parser.add_argument('--report_html')
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41 parser.add_argument('--log')
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42 args = parser.parse_args()
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43 projectName=args.projectName
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44 author=args.author
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45 targetFile=args.targetFile
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46 rawDir=args.rawDir
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47 featuresToRemove=args.featuresToRemove
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48 varInt=args.varInt
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49 condRef=args.condRef
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50 batch=args.batch
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51 alpha=args.alpha
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52 pAdjustMethod=args.pAdjustMethod
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53 cpmCutoff=args.cpmCutoff
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54 geneSelection=args.geneSelection
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55 normalizationMethod=args.normalizationMethod
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56 colors=args.colors
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3
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57 forceCairoGraph=args.forceCairoGraph
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0
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58 figures_html=args.figures_html
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59 figures_html_files_path=args.figures_html_files_path
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60 tables_html=args.tables_html
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61 tables_html_files_path=args.tables_html_files_path
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62 rdata=args.rdata
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63 report_html=args.report_html
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64 log=args.log
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65 #Print the parameters selected
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66 print("Wrapper arguments: %s") %(args)
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67
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68 #Get the working directory path
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69 working_directory = os.getcwd()
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70 #Get the script directory path
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71 script_directory=os.path.dirname(os.path.realpath(__file__))
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72
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73 #Unzip files from rawDir
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74 rawDir_unzipped_path=working_directory+"/rawDir_unzipped"
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75 os.mkdir(rawDir_unzipped_path)
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76 unzip_cmd="unzip -j %s -d %s" % (rawDir,rawDir_unzipped_path) #-j arg: junk paths
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77 os.system(unzip_cmd)
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78
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79 #Create the command
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80 cmd="Rscript --no-save --no-restore %s/template_script_edgeR_CL.r --projectName %s --author %s " % (script_directory,projectName,author)
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81 cmd+="--targetFile %s --rawDir %s --featuresToRemove %s --varInt %s --condRef %s " % (targetFile,rawDir_unzipped_path,featuresToRemove,varInt,condRef)
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82 if batch and batch!="NULL":
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83 cmd+="--batch %s " % (batch)
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84 if alpha:
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85 cmd+="--alpha %s " % (alpha)
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86 if pAdjustMethod:
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87 cmd+="--pAdjustMethod %s " % (pAdjustMethod)
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88 if cpmCutoff:
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89 cmd+="--cpmCutoff %s " % (cpmCutoff)
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90 if geneSelection:
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91 cmd+="--gene.selection %s " % (geneSelection)
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92 if normalizationMethod:
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93 cmd+="--normalizationMethod %s " % (normalizationMethod)
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94 if colors:
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95 cmd+="--colors %s " % (colors)
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3
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96 if forceCairoGraph:
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97 cmd+="--forceCairoGraph %s " % (forceCairoGraph)
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0
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98 cmd+="> %s 2>&1" % (log)
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99 print("Rscript command: %s") % (cmd)
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100 os.system(cmd)
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101
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102 #Get output files
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103 os.mkdir(figures_html_files_path)
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104 os.mkdir(tables_html_files_path)
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105 rsync_figures_dir_cmd="rsync -r figures/* %s/." % (figures_html_files_path)
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106 rsync_tables_dir_cmd="rsync -r tables/* %s/." % (tables_html_files_path)
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107 os.system(rsync_figures_dir_cmd)
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108 os.system(rsync_tables_dir_cmd)
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109 figures_html_create_cmd="python %s/make_html.py --tool SARTools_edgeR --output_type Figures --output_dir %s --output_html %s" % (script_directory,figures_html_files_path,figures_html)
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110 tables_html_create_cmd="python %s/make_html.py --tool SARTools_edgeR --output_type Tables --output_dir %s --output_html %s" % (script_directory,tables_html_files_path,tables_html)
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111 os.system(figures_html_create_cmd)
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112 os.system(tables_html_create_cmd)
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113 rsync_rdata_file_cmd="rsync %s.RData %s" % (projectName,rdata)
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114 rsync_report_file_cmd="rsync %s_report.html %s" % (projectName,report_html)
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115 os.system(rsync_rdata_file_cmd)
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116 os.system(rsync_report_file_cmd)
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117
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118 print("End of galaxy wrapper")
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119
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120 if __name__ == '__main__':
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121 main()
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122
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123
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