diff TEisotools-1.1.a/commons/core/coord/MapUtils.py @ 16:836ce3d9d47a draft default tip

Uploaded

--- a/TEisotools-1.1.a/commons/core/coord/MapUtils.py	Thu Jul 21 07:36:44 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,223 +0,0 @@
-# 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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