except:
pass
-import sys, optparse
-from commoncode import readDataset
+import sys
+import optparse
+import ReadDataset
+from commoncode import getConfigParser, getConfigOption, getConfigBoolOption, getConfigIntOption
PLUS_COLOR = "0,0,255"
MINUS_COLOR = "255,0,0"
if not argv:
argv = sys.argv
- verstring = "%prog: version 3.1"
+ verstring = "makebedfromrds: version 3.2"
print verstring
doPairs = False
usage = "usage: %prog trackLabel rdsFile bamFile [options]"
- parser = optparse.OptionParser(usage=usage)
- parser.add_option("--nouniq", action="store_false", dest="withUniqs")
- parser.add_option("--nomulti", action="store_false", dest="withMulti")
- parser.add_option("--splices", action="store_true", dest="doSplices")
- parser.add_option("--spliceColor", action="store_true", dest="doSpliceColor")
- parser.add_option("--flag", dest="withFlag")
- parser.add_option("--flaglike", action="store_true", dest="useFlagLike")
- parser.add_option("--pairs", type="int", dest="pairDist")
- parser.add_option("--cache", type="int", dest="cachePages")
- parser.add_option("--enforceChr", action="store_true", dest="enforceChr")
- parser.add_option("--chrom", action="append", dest="chromList")
- parser.add_option("--strand", dest="strand")
- parser.add_option("-r", "--region", dest="region", type="string",
- help="samtools region string")
- parser.set_defaults(withUniqs=True, withMulti=True, doSplices=False, doSpliceColor=False,
- pairDist=None, withFlag="", useFlagLike=False, enforceChr=False,
- senseStrand="", allChrom=True, doCache=False, cachePages=100000,
- chromList=[])
+ parser = getParser(usage)
(options, args) = parser.parse_args(argv[1:])
try:
options.allChrom, options.doCache, options.cachePages, options.chromList)
+def getParser(usage):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--nouniq", action="store_false", dest="withUniqs")
+ parser.add_option("--nomulti", action="store_false", dest="withMulti")
+ parser.add_option("--splices", action="store_true", dest="doSplices")
+ parser.add_option("--spliceColor", action="store_true", dest="doSpliceColor")
+ parser.add_option("--flag", dest="withFlag")
+ parser.add_option("--flaglike", action="store_true", dest="useFlagLike")
+ parser.add_option("--pairs", type="int", dest="pairDist")
+ parser.add_option("--cache", type="int", dest="cachePages")
+ parser.add_option("--enforceChr", action="store_true", dest="enforceChr")
+ parser.add_option("--chrom", action="append", dest="chromList")
+ parser.add_option("--strand", dest="strand")
+
+ configParser = getConfigParser()
+ section = "makebedfromrds"
+ withUniqs = getConfigBoolOption(configParser, section, "withUniqs", True)
+ withMulti = getConfigBoolOption(configParser, section, "withMulti", False)
+ doSplices = getConfigBoolOption(configParser, section, "doSplices", False)
+ doSpliceColor = getConfigBoolOption(configParser, section, "doSpliceColor", False)
+ pairDist = getConfigOption(configParser, section, "pairDist", None)
+ withFlag = getConfigOption(configParser, section, "withFlag", "")
+ useFlagLike = getConfigBoolOption(configParser, section, "useFlagLike", False)
+ enforceChr = getConfigBoolOption(configParser, section, "enforceChr", False)
+ senseStrand = getConfigOption(configParser, section, "senseStrand", "")
+ allChrom = getConfigBoolOption(configParser, section, "allChrom", True)
+ doCache = getConfigBoolOption(configParser, section, "doCache", False)
+ cachePages = getConfigOption(configParser, section, "cachePages", 100000)
+
+ parser.set_defaults(withUniqs=withUniqs, withMulti=withMulti, doSplices=doSplices, doSpliceColor=doSpliceColor,
+ pairDist=pairDist, withFlag=withFlag, useFlagLike=useFlagLike, enforceChr=enforceChr,
+ senseStrand=senseStrand, allChrom=allChrom, doCache=doCache, cachePages=cachePages,
+ chromList=[])
+
+ return parser
+
+
def outputBedFromRds(trackType, rdsfile, outfilename, withUniqs=True, withMulti=True,
doSplices=False, doSpliceColor=False, doPairs=False, pairDist=1000000,
withFlag="", useFlagLike=False, enforceChr=False, senseStrand="",
sys.exit(1)
print "\nsample:"
- RDS = readDataset(rdsfile, verbose = True, cache=doCache)
+ RDS = ReadDataset.ReadDataset(rdsfile, verbose = True, cache=doCache)
#check that this is better than the dataset's default cache size
if cachePages > RDS.getDefaultCacheSize():
listLen = len(localList) - 1
localIndex = 0
while localIndex <= listLen:
+ read = localList[localIndex]
try:
- (leftpos, leftsense, leftweight, lPairID) = localList[localIndex]
+ leftpos = read["start"]
+ leftsense = read["sense"]
+ leftweight = read["weight"]
+ lPairID = read["pairID"]
leftstop = leftpos + readlength - 1
lpart = 1
startList = [leftpos]
stopList = [leftstop]
- except:
- (leftpos, LLstop, LRstart, leftstop, leftsense, lPairID) = localList[localIndex]
+ except KeyError:
+ leftpos = read["startL"]
+ LLstop = read["stopL"]
+ LRstart = read["startR"]
+ leftstop = read["stopL"]
+ leftsense = read["sense"]
+ lPairID = read["pairID"]
leftweight = 1.0
lpart = 2
startList = [leftpos, LRstart]
stopList = [LLstop, leftstop]
if localIndex < listLen:
+ read = localList[localIndex + 1]
try:
- (rightpos, rightsense, rightweight, rPairID) = localList[localIndex + 1]
+ rightpos = read["start"]
+ rightsense = read["sense"]
+ rightweight = read["weight"]
+ rPairID= read["pairID"]
rightstop = rightpos + readlength - 1
rpart = 1
rstartList = [rightpos]
rstopList = [rightstop]
- except:
- (rightpos, RLstop, RRstart, rightstop, rightsense, rPairID) = localList[localIndex + 1]
+ except KeyError:
+ rightpos = read["startL"]
+ RLstop = read["stopL"]
+ RRstart = read["startR"]
+ rightstop = read["stopR"]
+ rightsense = read["sense"]
+ rPairID = read["pairID"]
rightweight = 1.0
rpart = 2
rstartList = [rightpos, RRstart]
else:
hitDict = RDS.getReadsDict(fullChrom=True, chrom=achrom, flag=withFlag, withWeight=True, withID=True, doUniqs=withUniqs, doMulti=withMulti, readIDDict=False, flagLike=useFlagLike)
try:
- for (pos, sense, weight, readID) in hitDict[achrom]:
+ for read in hitDict[achrom]:
+ pos = read["start"]
+ sense = read["sense"]
+ readID = read["readID"]
splitReadWrite(outfile, achrom, 1, [pos], [pos + readlength - 1], sense, readID, PLUS_COLOR, MINUS_COLOR)
index += 1
except:
spliceDict = RDS.getSplicesDict(fullChrom=True, chrom=achrom, flag=withFlag, withID=True, flagLike=useFlagLike)
if achrom not in spliceDict:
continue
- for (readstart, Lstop, Rstart, readstop, rsense, readName) in spliceDict[achrom]:
+ for read in spliceDict[achrom]:
+ readstart = read["startL"]
+ Lstop = read["stopL"]
+ Rstart = read["startR"]
+ readstop = read["stopR"]
+ rsense = read["sense"]
+ readName = read["readID"]
splitReadWrite(outfile, achrom, 2, [readstart, Rstart], [Lstop, readstop], rsense, readName, PLUS_COLOR, MINUS_COLOR)
index += 1
spliceDict = RDS.getSplicesDict(fullChrom=True, chrom=achrom, flag=withFlag, withID=True, flagLike=useFlagLike)
if achrom not in spliceDict:
continue
- for (readstart, Lstop, Rstart, readstop, rsense, readName) in spliceDict[achrom]:
+ for read in spliceDict[achrom]:
+ readstart = read["startL"]
+ Lstop = read["stopL"]
+ Rstart = read["startR"]
+ readstop = read["stopR"]
+ rsense = read["sense"]
+ readName = read["readID"]
splitReadWrite(outfile, achrom, 2, [readstart, Rstart], [Lstop, readstop], rsense, readName, PLUS_COLOR, MINUS_COLOR)
index += 1
projects / erange.git / blobdiff