def spliceFromCoords( genomeFile, coordFile, obsFile ):
genomeFileHandler = open( genomeFile, "r" )
obsFileHandler = open( obsFile, "w" )
dChr2Maps = MapUtils.getDictPerSeqNameFromMapFile( coordFile )
while True:
bs = Bioseq()
bs.read( genomeFileHandler )
if bs.sequence == None:
break
if dChr2Maps.has_key( bs.header ):
lCoords = MapUtils.getMapListSortedByIncreasingMinThenMax( dChr2Maps[ bs.header ] )
splicedSeq = ""
currentSite = 0
for iMap in lCoords:
minSplice = iMap.getMin() - 1
if minSplice > currentSite:
splicedSeq += bs.sequence[ currentSite : minSplice ]
currentSite = iMap.getMax()
splicedSeq += bs.sequence[ currentSite : ]
bs.sequence = splicedSeq
bs.write( obsFileHandler )
genomeFileHandler.close()
obsFileHandler.close()
def convertFastaHeadersFromChkToChr( inFile, mapFile, outFile ):
inFileHandler = open( inFile, "r" )
outFileHandler = open( outFile, "w" )
dChunk2Map = MapUtils.getDictPerNameFromMapFile( mapFile )
iConvCoord = ConvCoord()
while True:
line = inFileHandler.readline()
if line == "":
break
if line[0] == ">":
if "{Fragment}" not in line:
outFileHandler.write( line )
continue
chkName = line.split(" ")[1]
chrName = dChunk2Map[ chkName ].seqname
lCoordPairs = line.split(" ")[3].split(",")
lRangesOnChk = []
for i in lCoordPairs:
iRange = Range( chkName, int(i.split("..")[0]), int(i.split("..")[1]) )
lRangesOnChk.append( iRange )
lRangesOnChr = []
for iRange in lRangesOnChk:
lRangesOnChr.append( iConvCoord.getRangeOnChromosome( iRange, dChunk2Map ) )
newHeader = line[1:-1].split(" ")[0]
newHeader += " %s" % ( chrName )
newHeader += " {Fragment}"
newHeader += " %i..%i" % ( lRangesOnChr[0].start, lRangesOnChr[0].end )
for iRange in lRangesOnChr[1:]:
newHeader += ",%i..%i" % ( iRange.start, iRange.end )
outFileHandler.write( ">%s\n" % ( newHeader ) )
else:
outFileHandler.write( line )
inFileHandler.close()
outFileHandler.close()
def getSetListOverlappingCoord( self, seqName, start, end ):
lMaps = self.getListOverlappingCoord( seqName, start, end )
lSets = MapUtils.mapList2SetList( lMaps )
return lSets
def getSetListFromSeqName( self, seqName ):
lMaps = self.getListFromSeqName( seqName )
lSets = MapUtils.mapList2SetList( lMaps )
return lSets
