def mergeMatchesOnQueries(inFile, outFile):
mapFile = "%s.map" % ( inFile )
PathUtils.convertPathFileIntoMapFileWithQueryCoordsOnly( inFile, mapFile )
cmd = "mapOp"
cmd += " -q %s" % ( mapFile )
cmd += " -m"
cmd += " 2>&1 > /dev/null"
exitStatus = os.system( cmd )
if exitStatus != 0:
print "ERROR: mapOp returned %i" % ( exitStatus )
sys.exit(1)
os.remove( mapFile )
mergeFile = "%s.merge" % ( mapFile )
mergeFileHandler = open( mergeFile, "r" )
outFileHandler = open( outFile, "w" )
m = Map()
while True:
line = mergeFileHandler.readline()
if line == "":
break
m.reset()
m.setFromString( line, "\t" )
m.writeAsQueryOfPath( outFileHandler )
mergeFileHandler.close()
os.remove( mergeFile )
outFileHandler.close()
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
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
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()
