--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/LaunchRefAlign.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,208 @@
+#!/usr/bin/env python
+
+# Copyright INRA (Institut National de la Recherche Agronomique)
+# http://www.inra.fr
+# http://urgi.versailles.inra.fr
+#
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software.  You can  use, 
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info". 
+#
+# As a counterpart to the access to the source code and  rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty  and the software's author,  the holder of the
+# economic rights,  and the successive licensors  have only  limited
+# liability. 
+#
+# In this respect, the user's attention is drawn to the risks associated
+# with loading,  using,  modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean  that it is complicated to manipulate,  and  that  also
+# therefore means  that it is reserved for developers  and  experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or 
+# data to be ensured and,  more generally, to use and operate it in the 
+# same conditions as regards security. 
+#
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+
+from commons.core.LoggerFactory import LoggerFactory
+from commons.core.utils.RepetOptionParser import RepetOptionParser
+from commons.core.checker.ConfigChecker import ConfigRules
+from commons.core.checker.ConfigChecker import ConfigChecker
+import subprocess
+import os
+from commons.core.seq.Bioseq import Bioseq
+
+LOG_DEPTH = "repet.core.launchers"
+
+from commons.core.seq.BioseqDB import BioseqDB
+from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders
+
+
+class LaunchRefAlign(object):
+    """
+    Launch 'refalign' to build a master-slave multiple sequence alignment.
+    """
+    def __init__(self, inputFileName="", outFileName="", gapSize=10, match=10, mismatch=8, gapOpen=16, gapExtend=4, refseqName="", keepRefseq =False, verbosity=3 ):
+        self.inputFileName = inputFileName
+        self.outFileName=outFileName
+        self.gapSize = gapSize
+        self.match = match
+        self.mismatch = mismatch
+        self.gapOpen = gapOpen
+        self.gapExtend = gapExtend
+        self.gapExtend = gapExtend
+        self.refseqName = refseqName
+        self.keepRefseq = keepRefseq
+        self._verbosity = verbosity
+        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
+        
+    def setAttributesFromCmdLine(self):
+        description = "usage: LaunchRefalign.py [ options ]"
+        epilog = "\n -h: this help\n"
+        epilog += "\t -i: name of the input file (refseq is first, format='fasta')"
+        epilog += "\t -r: keep the reference sequence"
+        epilog += "\t -o: name of the output file (default=inFileName+'.fa_aln')"
+        epilog += "\t -v: verbosity (default=0)"
+        epilog += "\n\t"
+        parser = RepetOptionParser(description = description, epilog = epilog)
+        parser.add_option("-i", "--fasta",      dest = "inputFileName", action = "store",       type = "string", help = "input fasta file name [compulsory] [format: fasta]", default = "")
+        parser.add_option("-o", "--out",        dest = "outFileName",   action = "store",       type = "string", help = "output file name [default: <input>.out]", default = "")
+        parser.add_option("-r", "--keepRefseq", dest = "keepRefseq",    action = "store_true",                   help = "keep reference sequence [optional] [default: False]", default = False)
+        parser.add_option("-v", "--verbosity",  dest = "verbosity",     action = "store",       type = "int",    help = "verbosity [optional] [default: 1]", default = 1)
+        options = parser.parse_args()[0]
+        self._setAttributesFromOptions(options)
+        
+    def _setAttributesFromOptions(self, options):
+        self.inputFileName = options.inputFileName
+        self.setOutFileName = options.outFileName
+        self.keepRefseq = options.keepRefseq
+        self._verbosity = options.verbosity
+
+    def _checkOptions(self):
+        if self.inputFileName == "":
+            self._logAndRaise("ERROR: Missing input file name")
+    
+        if self.outFileName == "":
+            self.outFileName = "%s.fa_aln" % (self.inputFileName)
+            
+    def _logAndRaise(self, errorMsg):
+        self._log.error(errorMsg)
+        raise Exception(errorMsg)
+         
+    def _prepareRefAlign(self):
+        self.shortInputFileName = self.inputFileName+".shortH" 
+        self.refFileName= self.shortInputFileName + ".ref"
+        self.cpyFileName=self.shortInputFileName + ".cpy"
+        
+        file_db = open(self.shortInputFileName)
+        file_ref = open(self.refFileName,"w")
+        file_cpy = open(self.cpyFileName,"w")
+        
+        self._numseq=0
+        while 1:
+            seq=Bioseq()
+            seq.read(file_db)
+            if seq.sequence==None:
+                break
+            self._numseq+=1
+            if self._numseq==1:
+                seq.write(file_ref)
+            else:
+                seq.write(file_cpy)
+        file_db.close()
+        file_ref.close()
+        file_cpy.close()
+    
+    def _shortenHeaders(self):
+        self.csh = ChangeSequenceHeaders()
+        self.csh.setInputFile(self.inputFileName)
+        self.csh.setFormat("fasta")
+        self.csh.setStep(1)
+        self.csh.setPrefix("seq")
+        self.csh.setLinkFile(self.inputFileName+".shortHlink")
+        self.csh.setOutputFile(self.inputFileName+".shortH")
+        self.csh.setVerbosityLevel(self._verbosity-1)
+        self.csh.run()
+        
+        bsDB = BioseqDB(self.inputFileName+".shortH")
+        bsDB.upCase()
+        bsDB.save(self.inputFileName+".shortHtmp")
+        del bsDB
+        os.rename(self.inputFileName+".shortHtmp", self.inputFileName+".shortH")
+        
+    def _renameHeaders(self):
+        self.csh.setInputFile(self.inputFileName+".shortH.fa_aln")
+        self.csh.setFormat("fasta")
+        self.csh.setStep(2)
+        self.csh.setLinkFile(self.inputFileName+".shortHlink" )
+        self.csh.setOutputFile(self.outFileName)
+        self.csh.setVerbosityLevel(self._verbosity-1)
+        self.csh.run()
+          
+    def run(self):
+        LoggerFactory.setLevel(self._log, self._verbosity)
+        self._checkOptions()
+        self._log.info("START LaunchRefAlign")
+        self._log.debug("building a multiple alignment from '%s'..." % ( self.inputFileName))
+        
+        inputFileName = "%s/%s" % (os.getcwd(), os.path.basename(self.inputFileName))
+        if not os.path.exists(inputFileName):
+            os.symlink(self.inputFileName, inputFileName)
+        self.inputFileName = inputFileName
+        
+        self._shortenHeaders()
+        if self.keepRefseq:
+            self.refseqName="seq1"
+        self._prepareRefAlign()
+        
+        if self._numseq > 1:
+            cmd = "refalign %s %s -m %d -l %d -d %d -g %d -e %d" % (self.refFileName, self.cpyFileName, self.match, self.gapSize, self.mismatch, self.gapOpen, self.gapExtend)
+            
+            process = subprocess.Popen(cmd.split(' '), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+            self._log.debug("Running : %s" % cmd)
+            output = process.communicate()
+            self._log.debug("Output:\n%s" % output[0])
+            if process.returncode != 0:
+                self._logAndRaise("ERROR when launching '%s'" % cmd)
+            refseqNameParam = ""
+            if self.refseqName != "":
+                refseqNameParam = "-r %s " % (self.refseqName)
+            outFileName = self.inputFileName+".shortH.fa_aln"
+            #self.cpyFileName = os.path.join(os.getcwd(),os.path.basename(self.cpyFileName))
+            
+            self._log.info("Copy file path %s " % self.cpyFileName)
+            print("Copy file path %s " % self.cpyFileName)
+            cmd = "refalign2fasta.py -i %s.aligner %s-g d -o %s -v 1" % (self.cpyFileName, refseqNameParam, outFileName)
+            self._log.debug("Running : %s" % cmd)
+            process = subprocess.Popen(cmd.split(' '), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+            output = process.communicate()
+            self._log.debug("Output:\n%s" % output[0])
+            
+            if process.returncode != 0:
+                self._logAndRaise("ERROR when launching '%s'" % cmd)
+                
+            cmd = "rm -f "+ self.refFileName + " " + self.cpyFileName + " " + self.cpyFileName + ".aligner " + self.cpyFileName + ".oriented " + self.cpyFileName + ".refalign.stat"
+            os.system(cmd)
+            
+        else:
+            self._logAndRaise("Only one sequence available")
+            cmd = "echo empty"
+            
+        self._renameHeaders()
+        
+        for fileName in [self.inputFileName + ".shortH", self.inputFileName + ".shortHlink", self.inputFileName + ".shortH.fa_aln"]:
+            os.remove(fileName)
+        self._log.info("END LaunchRefAlign")
+        return 0
+        
+
+if __name__ == "__main__":
+    iLaunchRefAlign = LaunchRefAlign()
+    iLaunchRefAlign.setAttributesFromCmdLine()
+    iLaunchRefAlign.run()