view TEisotools-1.0/commons/core/coord/MapUtils.py @ 6:20ec0d14798e draft

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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". 
#
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# 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
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# 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
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# same conditions as regards security. 
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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