Mercurial > repos > yufei-luo > s_mart
view SMART/galaxy/WrappGetLetterDistribution.py @ 45:e454402ba9d9
Deleted selected files
author | m-zytnicki |
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date | Wed, 18 Sep 2013 08:51:22 -0400 |
parents | 94ab73e8a190 |
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#! /usr/bin/env python import os import sys import getopt from commons.core.checker.CheckerException import CheckerException SMART_PATH = "%s/SMART" % os.environ["REPET_PATH"] class WrappGetLetterDistribution(object): def __init__(self): self._inputFileName = "" self._inputFileFormat = "" self._outputFileName = "tmpOutputFile" self._csv = False def help( self ): print print "usage: %s [ options ]" % ( sys.argv[0] ) print "options:" print " -h: this help" print " -i: input file" print " -f: 'fasta' or 'fastq'" print " -c: CSV output file" print " -a: first PNG output file" print " -b: second PNG output file" print print "Exemple:" print print "1:\n\tpython WrappGetLetterDistribution.py -i inputFile.fasta -f fasta -c outputFile1.csv -a outputFile2.png -b outputFile3.png" print print "2:\n\tpython WrappGetLetterDistribution.py -i inputFile.fastq -f fastq -c outputFile1.csv -a outputFile2.png -b outputFile3.png" print print def setAttributesFromCommandLine(self): try: opts, args = getopt.getopt( sys.argv[1:], "hi:f:a:b:c:" ) except getopt.GetoptError, err: print str(err); sys.exit(1) for o, a in opts: if o == "-h": self.help() sys.exit(0) if o == "-i": self._inputFileName = a elif o == "-f": self._inputFileFormat = a elif o == "-c": self._outputFileNameCSV = a self._csv = True elif o == "-a": self._outputFileNamePNG = a elif o == "-b": self._outputFileNamePerNtPNG = a def checkAttributes(self): lMsg = [] if self._inputFileName == "" and not os.path.exists(self._inputFileName): lMsg.append("ERROR: This input file doesn't exist!") if self._inputFileFormat == "": lMsg.append("ERROR: No input file format specified in option!") if self._outputFileNamePNG == "": lMsg.append("ERROR: No output file.png specified in option!") if self._outputFileNamePerNtPNG == "": lMsg.append("ERROR: No output filePerNt.png specified in option!") if self._outputFileNameCSV == "" and self._csv == True : lMsg.append("ERROR: No output file.csv specified in option!") print ">>> lMsg " + str(lMsg) if lMsg != []: exp = CheckerException() exp.setMessages(lMsg) raise (exp) def _cleanWorkingDir(self, cDir): os.system("rm %s/tmpData* %s/tmpScript*" % (cDir, cDir)) def wrapp(self): self.checkAttributes() cDir = os.getcwd() if self._csv == True: os.system("python %s/Java/Python/getLetterDistribution.py -i %s -f %s -o %s/%s -c" % (SMART_PATH, self._inputFileName, self._inputFileFormat, cDir, self._outputFileName)) os.system("mv %s/%s.csv %s" % (cDir, self._outputFileName, self._outputFileNameCSV)) os.system("mv %s/%s.png %s" % (cDir, self._outputFileName, self._outputFileNamePNG)) os.system("mv %s/%sPerNt.png %s" % (cDir, self._outputFileName, self._outputFileNamePerNtPNG)) self._cleanWorkingDir(cDir) if __name__ == '__main__': launcher = WrappGetLetterDistribution() launcher.setAttributesFromCommandLine() launcher.wrapp()