Mercurial > repos > ntino-krampis > viralcloud
diff viral_assembly_annotation/viral_assembly.py @ 0:beaf42837914 draft
viral cloud resource galaxy tool definitions initial commit
author | ntino-krampis |
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date | Thu, 31 Jan 2013 13:41:35 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/viral_assembly_annotation/viral_assembly.py Thu Jan 31 13:41:35 2013 -0500 @@ -0,0 +1,38 @@ +#!/usr/bin/env python + +""" +Takes input from viral_assembly.xml and sends it to vir-assembly-pipeline.sh. +""" + +import os, sys, subprocess, tempfile, shutil + +def __prepare_input__(draftFilename,finalFilename,finalDir): + result = "%s/%s" % (finalDir,finalFilename) + + if draftFilename == "None": + os.system("sudo touch %s" % result) + else: + os.system("sudo cp %s %s" % (draftFilename,result)) + + return result + +def __main__(): + # Parse the command line options + (input_454,input_Sanger,input_Solexa,input_Solexa_tp,database,outputFasta) = sys.argv[1:] + + # Copy the input files to the VHTNGS location. If an input file was not given, create an empty dummy file as a replacement. + inputDir = "/usr/local/VHTNGS" + + input_454_ready = __prepare_input__(input_454,"input_454.sff",inputDir) + input_Sanger_ready = __prepare_input__(input_Sanger,"input_Sanger.fasta",inputDir) + input_Solexa_ready = __prepare_input__(input_Solexa,"input_Solexa.fastq",inputDir) + input_Solexa_tp_ready = __prepare_input__(input_Solexa_tp,"input_Solexa.fastq.trimpoints",inputDir) + + command = "/usr/local/VHTNGS/vir-assembly-pipeline.sh %s %s %s %s %s" % (input_454_ready,input_Sanger_ready,input_Solexa_ready,input_Solexa_tp_ready,database) + virAssemblyOutput = "/usr/local/VHTNGS/project/mapping/sample_hybrid_edited_refs_consensus.fasta" + os.system("sudo %s" % command) + os.system("sudo chmod 777 %s" % virAssemblyOutput) + os.system("sudo cp %s %s" % (virAssemblyOutput,outputFasta)) + +if __name__=="__main__": + __main__()