Mercurial > repos > lgueguen > sartools
view abims_sartools_edger_wrapper.py @ 1:fe0ee346b17d draft
RSEM process files corrected in pre_sartools.py
author | lgueguen |
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date | Wed, 26 Apr 2017 05:04:18 -0400 |
parents | 581d217c7337 |
children | de6d0b7c17af |
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#abims_sartools_edger_wrapper.py #Author: Loraine Gueguen # imports import os, argparse def main(): print("Start of galaxy wrapper") #Check R and Rscript are installed check_r_cmd="command -v R >/dev/null 2>&1 || { echo >&2 'This tool requires R but it is not installed. Aborting.'; exit 1; }" check_rscript_cmd="command -v Rscript >/dev/null 2>&1 || { echo >&2 'This tool requires Rscript but it is not installed. Aborting.'; exit 1; }" os.system(check_r_cmd) os.system(check_rscript_cmd) #Get arguments parser = argparse.ArgumentParser() parser.add_argument('--projectName') parser.add_argument('--author') parser.add_argument('--targetFile') parser.add_argument('--rawDir') parser.add_argument('--featuresToRemove') parser.add_argument('--varInt') parser.add_argument('--condRef') parser.add_argument('--batch') parser.add_argument('--alpha') parser.add_argument('--pAdjustMethod') parser.add_argument('--cpmCutoff') parser.add_argument('--geneSelection') parser.add_argument('--normalizationMethod') parser.add_argument('--colors') parser.add_argument('--figures_html') parser.add_argument('--figures_html_files_path') parser.add_argument('--tables_html') parser.add_argument('--tables_html_files_path') parser.add_argument('--rdata') parser.add_argument('--report_html') parser.add_argument('--log') args = parser.parse_args() projectName=args.projectName author=args.author targetFile=args.targetFile rawDir=args.rawDir featuresToRemove=args.featuresToRemove varInt=args.varInt condRef=args.condRef batch=args.batch alpha=args.alpha pAdjustMethod=args.pAdjustMethod cpmCutoff=args.cpmCutoff geneSelection=args.geneSelection normalizationMethod=args.normalizationMethod colors=args.colors figures_html=args.figures_html figures_html_files_path=args.figures_html_files_path tables_html=args.tables_html tables_html_files_path=args.tables_html_files_path rdata=args.rdata report_html=args.report_html log=args.log #Print the parameters selected print("Wrapper arguments: %s") %(args) #Get the working directory path working_directory = os.getcwd() #Get the script directory path script_directory=os.path.dirname(os.path.realpath(__file__)) #Unzip files from rawDir rawDir_unzipped_path=working_directory+"/rawDir_unzipped" os.mkdir(rawDir_unzipped_path) unzip_cmd="unzip -j %s -d %s" % (rawDir,rawDir_unzipped_path) #-j arg: junk paths os.system(unzip_cmd) #Create the command cmd="Rscript --no-save --no-restore %s/template_script_edgeR_CL.r --projectName %s --author %s " % (script_directory,projectName,author) cmd+="--targetFile %s --rawDir %s --featuresToRemove %s --varInt %s --condRef %s " % (targetFile,rawDir_unzipped_path,featuresToRemove,varInt,condRef) if batch and batch!="NULL": cmd+="--batch %s " % (batch) if alpha: cmd+="--alpha %s " % (alpha) if pAdjustMethod: cmd+="--pAdjustMethod %s " % (pAdjustMethod) if cpmCutoff: cmd+="--cpmCutoff %s " % (cpmCutoff) if geneSelection: cmd+="--gene.selection %s " % (geneSelection) if normalizationMethod: cmd+="--normalizationMethod %s " % (normalizationMethod) if colors: cmd+="--colors %s " % (colors) cmd+="> %s 2>&1" % (log) print("Rscript command: %s") % (cmd) os.system(cmd) #Get output files os.mkdir(figures_html_files_path) os.mkdir(tables_html_files_path) rsync_figures_dir_cmd="rsync -r figures/* %s/." % (figures_html_files_path) rsync_tables_dir_cmd="rsync -r tables/* %s/." % (tables_html_files_path) os.system(rsync_figures_dir_cmd) os.system(rsync_tables_dir_cmd) 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) 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) os.system(figures_html_create_cmd) os.system(tables_html_create_cmd) rsync_rdata_file_cmd="rsync %s.RData %s" % (projectName,rdata) rsync_report_file_cmd="rsync %s_report.html %s" % (projectName,report_html) os.system(rsync_rdata_file_cmd) os.system(rsync_report_file_cmd) print("End of galaxy wrapper") if __name__ == '__main__': main()