diff TEisotools-1.1.a/commons/core/coord/MapUtils.py @ 13:feef9a0db09d draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEisotools-1.1.a/commons/core/coord/MapUtils.py	Wed Jul 20 09:04:42 2016 -0400
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+# 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 os
+import sys
+from commons.core.coord.Map import Map
+from commons.core.coord.Set import Set
+from commons.core.checker.CheckerUtils import CheckerUtils
+
+
+## static methods manipulating Map instances
+#
+class MapUtils( object ):
+    
+    ## Return a Map list from a Map file
+    #
+    # @param mapFile string name of a Map file
+    # @return a list of Map instances
+    #
+    @staticmethod
+    def getMapListFromFile(mapFile):
+        lMaps = []
+        with open(mapFile, "r") as mapF:
+            for line in mapF:
+                iMap = Map()
+                iMap.setFromString(line)
+                lMaps.append(iMap)
+        return lMaps
+
+        
+    ## 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
+    #
+    @staticmethod
+    def getMapListSortedByIncreasingMinThenMax(lMaps):
+        return sorted(lMaps, key = lambda iMap: (iMap.getMin(), iMap.getMax()))
+    
+    
+    ## 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
+    #
+    @staticmethod
+    def getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax(lMaps):
+        return sorted(lMaps, key = lambda iMap: (iMap.getName(), iMap.getSeqname(), iMap.getMin(), iMap.getMax()))
+    
+    
+    ## Return a dictionary which keys are Map names and values the corresponding Map instances
+    #
+    # @param mapFile string input map file name
+    #
+    @staticmethod
+    def getDictPerNameFromMapFile(mapFile):
+        dName2Maps = {}
+        with open(mapFile) as mapFileHandler:
+            for line in mapFileHandler:
+                iMap = Map()
+                iMap.setFromString(line, "\t")
+                if dName2Maps.has_key(iMap.name):
+                    if iMap != dName2Maps[iMap.name]:
+                        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)
+                else:
+                    dName2Maps[iMap.name] = iMap
+        return dName2Maps
+    
+    
+    ## Give a list of Set instances from a list of Map instances
+    #
+    # @param lMaps list of Map instances
+    # @return lSets list of Set instances
+    #
+    @staticmethod
+    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
+    
+    
+    ## Merge the Map instances in a Map file using 'mapOp'
+    #
+    # @param mapFile string input map file name
+    #
+    @staticmethod
+    def mergeCoordsInFile(mapFile, outFile):
+        if not CheckerUtils.isExecutableInUserPath("mapOp"):
+            msg = "WARNING: can't find executable 'mapOp'"
+            sys.stderr.write("%s\n" % msg)
+        else:
+            cmd = "mapOp"
+            cmd += " -q %s" % mapFile
+            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" % mapFile, outFile)
+
+    
+    ## Return a dictionary which keys are Map seqnames and values the corresponding Map instances
+    #
+    # @param mapFile string input map file name
+    #
+    @staticmethod
+    def getDictPerSeqNameFromMapFile(mapFile):
+        dSeqName2Maps = {}
+        with open(mapFile) as mapFileHandler:
+            for line in mapFileHandler:
+                iMap = Map()
+                iMap.setFromString(line, "\t")
+                if not dSeqName2Maps.has_key(iMap.seqname):
+                    dSeqName2Maps[iMap.seqname] = []
+                dSeqName2Maps[iMap.seqname].append(iMap)
+        return dSeqName2Maps
+    
+    
+    ## Convert an Map file into a Set file
+    #
+    # @param mapFileName string input map file name
+    # @param setFileName string output set file name
+    #
+    @staticmethod
+    def convertMapFileIntoSetFile(mapFileName, setFileName = ""):
+        if not setFileName:
+            setFileName = "%s.set" % mapFileName
+        setFileHandler = open(setFileName, "w")
+        count = 0
+        iMap = Map()
+        with open(mapFileName, "r") as mapFileHandler:
+            for line in mapFileHandler:
+                count += 1
+                iMap.setFromString(line)
+                iSet = Set()
+                iSet.id = count
+                iSet.name = iMap.getName()
+                iSet.seqname = iMap.getSeqname()
+                iSet.start = iMap.getStart()
+                iSet.end = iMap.getEnd()
+                iSet.write(setFileHandler)
+        setFileHandler.close()
+        
+
+    ## 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"' 
+    #
+    @staticmethod
+    def writeListInFile(lMaps, fileName, mode = "w"):
+        fileHandler = open(fileName, mode)
+        for iMap in lMaps:
+            iMap.write(fileHandler)
+        fileHandler.close()
+        
+    
+    ## Get the length of the shorter annotation in map file
+    #
+    # @param mapFile string input map file name
+    #
+    @staticmethod
+    def getMinLengthOfMapFile(mapFileName):
+        lSizes = []
+        with open(mapFileName) as fH:
+            for line in fH:
+                start = int(line.split('\t')[2])
+                end = int(line.split('\t')[3])
+                lSizes.append(end - start + 1)
+        return min(lSizes)
+
+
+    ## Get the length of the longest annotation in map file
+    #
+    # @param mapFile string input map file name
+    #
+    @staticmethod
+    def getMaxLengthOfMapFile(mapFileName):
+        maxLength = 0
+        with open(mapFileName) as fH:
+            for line in fH:
+                start = int(line.split('\t')[2])
+                end = int(line.split('\t')[3])
+                maxLength = max(maxLength, end - start + 1)
+        return maxLength
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