s_mart: smart_toolShed/commons/core/coord/MapUtils.py comparison

comparison smart_toolShed/commons/core/coord/MapUtils.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

author	yufei-luo
date	Thu, 17 Jan 2013 10:52:14 -0500
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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 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

Mercurial > repos > yufei-luo > s_mart

comparison smart_toolShed/commons/core/coord/MapUtils.py @ 0:e0f8dcca02ed