--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/coord/MapUtils.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,246 @@
+# 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.
+
+
+import sys
+import os
+from commons.core.coord.Map import Map
+from commons.core.coord.Set import Set
+try:
+    from commons.core.checker.CheckerUtils import CheckerUtils
+except ImportError:
+    pass
+
+
+## static methods manipulating Map instances
+#
+class MapUtils( object ):
+    
+    ## Return a list of Map instances sorted in increasing order according to the min, then the max, and finally their initial order
+    #
+    # @param lMaps list of Map instances
+    #
+    def getMapListSortedByIncreasingMinThenMax( lMaps ):
+        return sorted( lMaps, key=lambda iMap: ( iMap.getMin(), iMap.getMax() ) )    
+    
+    getMapListSortedByIncreasingMinThenMax = staticmethod( getMapListSortedByIncreasingMinThenMax )
+    
+    
+    ## Return a list of Map instances sorted in increasing order according to the name, then the seqname, then the min, then the max
+    #
+    # @param lMaps list of Map instances
+    #
+    def getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax( lMaps ):
+        return sorted( lMaps, key=lambda iMap: ( iMap.getName(), iMap.getSeqname(), iMap.getMin(), iMap.getMax() ) )    
+    
+    getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax = staticmethod( getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax )
+    
+    
+    ## Return a dictionary which keys are Map names and values the corresponding Map instances
+    #
+    def getDictPerNameFromMapFile( mapFile ):
+        dName2Maps = {}
+        mapFileHandler = open( mapFile, "r" )
+        while True:
+            line = mapFileHandler.readline()
+            if line == "":
+                break
+            iMap = Map()
+            iMap.setFromString( line, "\t" )
+            if dName2Maps.has_key( iMap.name ):
+                if iMap == dName2Maps[ iMap.name ]:
+                    continue
+                else:
+                    msg = "ERROR: in file '%s' two different Map instances have the same name '%s'" % ( mapFile, iMap.name )
+                    sys.stderr.write( "%s\n" % ( msg ) )
+                    sys.exit(1)
+            dName2Maps[ iMap.name ] = iMap
+        mapFileHandler.close()
+        return dName2Maps
+    
+    getDictPerNameFromMapFile = staticmethod( getDictPerNameFromMapFile )
+
+    
+    ## Give a list of Set instances from a list of Map instances
+    #
+    # @param lMaps list of Map instances
+    # @return lSets list of Set instances
+    #
+    def mapList2SetList( lMaps ):
+        lSets = []
+        c = 0
+        for iMap in lMaps:
+            c += 1
+            iSet = Set()
+            iSet.id = c
+            iSet.name = iMap.getName()
+            iSet.seqname = iMap.getSeqname()
+            iSet.start = iMap.getStart()
+            iSet.end = iMap.getEnd()
+            lSets.append( iSet )
+        return lSets
+    
+    mapList2SetList = staticmethod( mapList2SetList )
+    
+    
+    ## Merge the Map instances in a Map file using 'mapOp'
+    #
+    def mergeCoordsInFile( inFile, outFile ):
+        if not sys.modules.has_key( "commons.core.checker.CheckerUtils" ):
+            msg = "WARNING: can't find module 'CheckerUtils'"
+            sys.stderr.write( "%s\n" % msg )
+        elif not CheckerUtils.isExecutableInUserPath( "mapOp" ):
+            msg = "WARNING: can't find executable 'mapOp'"
+            sys.stderr.write( "%s\n" % msg )
+        else:
+            cmd = "mapOp"
+            cmd += " -q %s" % ( inFile )
+            cmd += " -m"
+            cmd += " 2>&1 > /dev/null"
+            returnStatus = os.system( cmd )
+            if returnStatus != 0:
+                print "ERROR: mapOp returned %i" % ( returnStatus )
+                sys.exit(1)
+            os.rename( "%s.merge" % inFile,
+                       outFile )
+            
+    mergeCoordsInFile = staticmethod( mergeCoordsInFile )
+    
+    
+    ## Return a dictionary which keys are Map seqnames and values the corresponding Map instances
+    #
+    def getDictPerSeqNameFromMapFile( mapFile ):
+        dSeqName2Maps = {}
+        mapFileHandler = open( mapFile, "r" )
+        while True:
+            line = mapFileHandler.readline()
+            if line == "":
+                break
+            iMap = Map()
+            iMap.setFromString( line, "\t" )
+            if not dSeqName2Maps.has_key( iMap.seqname ):
+                dSeqName2Maps[ iMap.seqname ] = []
+            dSeqName2Maps[ iMap.seqname ].append( iMap )
+        mapFileHandler.close()
+        return dSeqName2Maps
+    
+    getDictPerSeqNameFromMapFile = staticmethod( getDictPerSeqNameFromMapFile )
+    
+    
+    ## Convert an Map file into a Set file
+    #
+    # @param mapFile string input map file name
+    # @param setFile string output set file name
+    #
+    def convertMapFileIntoSetFile( mapFileName, setFileName = "" ):
+        if setFileName == "":
+            setFileName = "%s.set" % mapFileName
+        mapFileHandler = open( mapFileName, "r" )
+        setFileHandler = open( setFileName, "w" )
+        iMap = Map()
+        count = 0
+        while True:
+            line = mapFileHandler.readline()
+            if line == "":
+                break
+            iMap.setFromString(line)
+            count += 1
+            iSet = Set()
+            iSet.id = count
+            iSet.name = iMap.getName()
+            iSet.seqname = iMap.getSeqname()
+            iSet.start = iMap.getStart()
+            iSet.end = iMap.getEnd()
+            iSet.write(setFileHandler)
+        mapFileHandler.close()
+        setFileHandler.close()
+        
+    convertMapFileIntoSetFile = staticmethod( convertMapFileIntoSetFile )
+    
+    ## Write Map instances contained in the given list
+    #
+    # @param lMaps list of Map instances
+    # @param fileName a file name
+    # @param mode the open mode of the file '"w"' or '"a"' 
+    #
+    def writeListInFile(lMaps, fileName, mode="w"):
+        fileHandler = open(fileName, mode)
+        for iMap in lMaps:
+            iMap.write(fileHandler)
+        fileHandler.close()
+        
+    writeListInFile = staticmethod( writeListInFile )
+
+    
+    ## Get the length of the shorter seq in map file
+    #
+    # @param mapFileName
+    # @param mode the open mode of the file '"w"' or '"a"' 
+    #
+    def getMinLengthOfMapFile(self, mapFileName):
+        fileHandler = open(mapFileName, "r")
+        line = fileHandler.readline()
+        start = int (line.split('\t')[2])
+        end = int (line.split('\t')[3])
+        min = end - start + 1
+        while True:
+            line = fileHandler.readline()
+            if line == "":
+                break
+            start = int (line.split('\t')[2])
+            end = int (line.split('\t')[3])
+            currentMin = end - start + 1
+            if min >= currentMin:
+                min = currentMin
+        fileHandler.close()
+        return min
+
+    ## Get the max length of the shorter seq in map file
+    #
+    # @param mapFileName
+    # @param mode the open mode of the file '"w"' or '"a"' 
+    #
+    def getMaxLengthOfMapFile(self, mapFileName):
+        fileHandler = open(mapFileName, "r")
+        line = fileHandler.readline()
+        start = int (line.split('\t')[2])
+        end = int (line.split('\t')[3])
+        max = end - start + 1
+        while True:
+            line = fileHandler.readline()
+            if line == "":
+                break
+            start = int (line.split('\t')[2])
+            end = int (line.split('\t')[3])
+            currentMax = end - start + 1
+            if max <= currentMax:
+                max = currentMax
+        fileHandler.close()
+        return max
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