def parseOptions(self, options ):
timer = gtime.TimeKeeper()
if(options.subparser_name == 'parse'):
# parse raw input
print "*******************************************************************************"
print " [[GroopM %s]] Running in data parsing mode..." % self.GMVersion
print "*******************************************************************************"
# check this here:
if len(options.bamfiles) < 3:
print "Sorry, You must supply at least 3 bamFiles to use GroopM. (You supplied %d)\n Exiting..." % len(options.bamfiles)
return
GMdata = mstore.GMDataManager()
success = GMdata.createDB(options.bamfiles,
options.reference,
options.dbname,
options.cutoff,
timer,
force=options.force,
threads=options.threads)
if not success:
print options.dbname,"not updated"
elif(options.subparser_name == 'core'):
# make bin cores
print "*******************************************************************************"
print " [[GroopM %s]] Running in core creation mode..." % self.GMVersion
print "*******************************************************************************"
CE = cluster.ClusterEngine(options.dbname,
timer,
force=options.force,
finalPlot=options.plot,
plot=options.multiplot,
minSize=options.size,
minVol=options.bp)
if options.graphfile is None:
gf = ""
else:
gf=options.graphfile
CE.makeCores(coreCut=options.cutoff,
gf=gf)
elif(options.subparser_name == 'refine'):
# refine bin cores
print "*******************************************************************************"
print " [[GroopM %s]] Running in core refining mode..." % self.GMVersion
print "*******************************************************************************"
bids = []
#if options.bids is not None:
# bids = options.bids
auto = options.auto
transform=True^options.no_transform
RE = refine.RefineEngine(timer,
dbFileName=options.dbname,
transform=transform,
bids=bids,
loadContigNames=True)
if options.plot:
pfx="REFINED"
else:
pfx=""
print "Refine bins"
RE.refineBins(timer,
auto=auto,
saveBins=True,
plotFinal=pfx)
elif(options.subparser_name == 'recruit'):
# make bin cores
print "*******************************************************************************"
print " [[GroopM %s]] Running in bin expansion mode..." % self.GMVersion
print "*******************************************************************************"
RE = refine.RefineEngine(timer,
dbFileName=options.dbname,
getUnbinned=True,
loadContigNames=False,
cutOff=options.cutoff)
RE.recruitWrapper(timer,
inclusivity=options.inclusivity,
step=options.step,
saveBins=True)
elif(options.subparser_name == 'extract'):
# Extract data
print "*******************************************************************************"
print " [[GroopM %s]] Running in '%s' extraction mode..." % (self.GMVersion, options.mode)
print "*******************************************************************************"
bids = []
if options.bids is not None:
bids = options.bids
BX = groopmUtils.GMExtractor(options.dbname,
bids=bids,
folder=options.out_folder
)
if(options.mode=='contigs'):
BX.extractContigs(timer,
fasta=options.data,
prefix=options.prefix,
cutoff=options.cutoff)
elif(options.mode=='reads'):
BX.extractReads(timer,
bams=options.data,
prefix=options.prefix,
mixBams=options.mix_bams,
mixGroups=options.mix_groups,
mixReads=options.mix_reads,
interleaved=options.interleave,
bigFile=options.no_gzip,
headersOnly=options.headers_only,
minMapQual=options.mapping_quality,
maxMisMatches=options.max_distance,
useSuppAlignments=options.use_supplementary,
useSecondaryAlignments=options.use_secondary,
verbose=options.verbose,
threads=options.threads)
else:
raise ExtractModeNotAppropriateException("mode: "+ options.mode + " is unknown")
elif(options.subparser_name == 'merge'):
# make bin cores
print "*******************************************************************************"
print " [[GroopM %s]] Running in bin merging mode..." % self.GMVersion
print "*******************************************************************************"
BM = binManager.BinManager(dbFileName=options.dbname)
BM.loadBins(timer, makeBins=True, silent=False)
BM.merge(options.bids, options.force, saveBins=True)
elif(options.subparser_name == 'split'):
# make bin cores
print "*******************************************************************************"
print " [[GroopM %s]] Running in bin splitting mode..." % self.GMVersion
print "*******************************************************************************"
BM = binManager.BinManager(dbFileName=options.dbname)
BM.loadBins(timer, makeBins=True, silent=False)
BM.split(options.bid, options.parts, mode=options.mode, saveBins=True, auto=options.force)
elif(options.subparser_name == 'delete'):
# make bin cores
print "*******************************************************************************"
print " [[GroopM %s]] Running in bin deleting mode..." % self.GMVersion
print "*******************************************************************************"
BM = binManager.BinManager(dbFileName=options.dbname)
BM.loadBins(timer, makeBins=True, silent=True)#, bids=options.bids)
BM.deleteBins(options.bids, force=options.force, saveBins=True, freeBinnedRowIndices=True)
elif(options.subparser_name == 'plot'):
print "*******************************************************************************"
print " [[GroopM %s]] Running in bin plotting mode..." % self.GMVersion
print "*******************************************************************************"
BM = binManager.BinManager(dbFileName=options.dbname)
if options.bids is None:
bids = []
else:
bids = options.bids
BM.loadBins(timer, makeBins=True, silent=False, bids=bids, loadContigNames=False)
BM.setColorMap(options.cm)
BM.plotBins(FNPrefix=options.tag,
plotEllipsoid=True,
ignoreContigLengths=options.points,
folder=options.folder)
elif(options.subparser_name == 'explore'):
# make bin cores
print "*******************************************************************************"
print " [[GroopM %s]] Running in bin '%s' explorer mode..." % (self.GMVersion, options.mode)
print "*******************************************************************************"
transform=True^options.no_transform
bids = []
if options.bids is not None:
bids = options.bids
BE = groopmUtils.BinExplorer(options.dbname,
bids=bids,
transform=transform,
cmstring=options.cm,
ignoreContigLengths=options.points)
if(options.mode == 'binpoints'):
BE.plotPoints(timer)
elif(options.mode == 'binids'):
BE.plotIds(timer)
elif(options.mode == 'allcontigs'):
BE.plotContigs(timer, coreCut=options.cutoff, all=True)
elif(options.mode == 'unbinnedcontigs'):
BE.plotUnbinned(timer, coreCut=options.cutoff)
elif(options.mode == 'binnedcontigs'):
BE.plotContigs(timer, coreCut=options.cutoff)
elif(options.mode == 'binassignments'):
BE.plotBinAssignents(timer, coreCut=options.cutoff)
elif(options.mode == 'compare'):
BE.plotCompare(timer, coreCut=options.cutoff)
elif (options.mode == 'together'):
BE.plotTogether(timer, coreCut=options.cutoff, doMers=options.kmers)
elif (options.mode == 'sidebyside'):
BE.plotSideBySide(timer, coreCut=options.cutoff)
else:
print "**Error: unknown mode:",options.mode
elif(options.subparser_name == 'flyover'):
# make bin cores
print "*******************************************************************************"
print " [[GroopM %s]] Making a flyover..." % self.GMVersion
print "*******************************************************************************"
bids = []
if options.bids is not None:
bids = options.bids
BE = groopmUtils.BinExplorer(options.dbname,
bids=bids,
transform=True,
ignoreContigLengths=options.points)
BE.plotFlyOver(timer,
fps=options.fps,
totalTime=options.totalTime,
percentFade=options.firstFade,
prefix=options.prefix,
showColorbar=options.colorbar,
title=options.title,
coreCut=options.cutoff,
format=options.format)
elif(options.subparser_name == 'highlight'):
# make bin cores
print "*******************************************************************************"
print " [[GroopM %s]] Running in highlighter mode..." % self.GMVersion
print "*******************************************************************************"
bids = []
if options.bids is not None:
bids = options.bids
BE = groopmUtils.BinExplorer(options.dbname,
bids=bids,
binLabelsFile = options.binlabels,
contigColorsFile = options.contigcolors,
ignoreContigLengths=options.points)
BE.plotHighlights(timer,
options.elevation,
options.azimuth,
options.file,
options.filetype,
options.dpi,
drawRadius=options.radius,
show=options.show,
coreCut=options.cutoff,
testing=options.place
)
elif(options.subparser_name == 'print'):
BM = binManager.BinManager(dbFileName=options.dbname)
bids = []
if options.bids is not None:
bids = options.bids
BM.loadBins(timer, getUnbinned=options.unbinned, makeBins=True, silent=True, bids=bids)
BM.printBins(options.format, fileName=options.outfile)
elif(options.subparser_name == 'dump'):
print "*******************************************************************************"
print " [[GroopM %s]] Running in data dumping mode..." % self.GMVersion
print "*******************************************************************************"
# prep fields. Do this first cause users are mot likely to
# mess this part up!
allowable_fields = ['names', 'mers', 'gc', 'coverage', 'tcoverage', 'ncoverage', 'lengths', 'bins', 'all']
fields = options.fields.split(',')
for field in fields:
if field not in allowable_fields:
print "ERROR: field '%s' not recognised. Allowable fields are:" % field
print '\t',",".join(allowable_fields)
return
if options.separator == '\\t':
separator = '\t'
else:
separator = options.separator
DM = GMDataManager()
DM.dumpData(options.dbname,
fields,
options.outfile,
separator,
not options.no_headers)
return 0
def parseOptions(self, options):
timer = gtime.TimeKeeper()
if (options.subparser_name == 'parse'):
# parse raw input
print "*******************************************************************************"
print " [[GroopM %s]] Running in data parsing mode..." % self.GMVersion
print "*******************************************************************************"
# check this here:
if len(options.bamfiles) < 3:
print "Sorry, You must supply at least 3 bamFiles to use GroopM. (You supplied %d)\n Exiting..." % len(
options.bamfiles)
return
GMdata = mstore.GMDataManager()
success = GMdata.createDB(options.bamfiles,
options.reference,
options.dbname,
options.cutoff,
timer,
force=options.force,
threads=options.threads)
if not success:
print options.dbname, "not updated"
elif (options.subparser_name == 'core'):
# make bin cores
print "*******************************************************************************"
print " [[GroopM %s]] Running in core creation mode..." % self.GMVersion
print "*******************************************************************************"
CE = cluster.ClusterEngine(options.dbname,
timer,
force=options.force,
finalPlot=options.plot,
plot=options.multiplot,
minSize=options.size,
minVol=options.bp)
if options.graphfile is None:
gf = ""
else:
gf = options.graphfile
CE.makeCores(coreCut=options.cutoff, gf=gf)
elif (options.subparser_name == 'refine'):
# refine bin cores
print "*******************************************************************************"
print " [[GroopM %s]] Running in core refining mode..." % self.GMVersion
print "*******************************************************************************"
bids = []
#if options.bids is not None:
# bids = options.bids
auto = options.auto
transform = True ^ options.no_transform
RE = refine.RefineEngine(timer,
dbFileName=options.dbname,
transform=transform,
bids=bids,
loadContigNames=True)
if options.plot:
pfx = "REFINED"
else:
pfx = ""
print "Refine bins"
RE.refineBins(timer, auto=auto, saveBins=True, plotFinal=pfx)
elif (options.subparser_name == 'recruit'):
# make bin cores
print "*******************************************************************************"
print " [[GroopM %s]] Running in bin expansion mode..." % self.GMVersion
print "*******************************************************************************"
RE = refine.RefineEngine(timer,
dbFileName=options.dbname,
getUnbinned=True,
loadContigNames=False,
cutOff=options.cutoff)
RE.recruitWrapper(timer,
inclusivity=options.inclusivity,
step=options.step,
saveBins=True)
elif (options.subparser_name == 'extract'):
# Extract data
print "*******************************************************************************"
print " [[GroopM %s]] Running in '%s' extraction mode..." % (
self.GMVersion, options.mode)
print "*******************************************************************************"
bids = []
if options.bids is not None:
bids = options.bids
BX = groopmUtils.GMExtractor(options.dbname,
bids=bids,
folder=options.out_folder)
if (options.mode == 'contigs'):
BX.extractContigs(timer,
fasta=options.data,
prefix=options.prefix,
cutoff=options.cutoff)
elif (options.mode == 'reads'):
BX.extractReads(timer,
bams=options.data,
prefix=options.prefix,
mixBams=options.mix_bams,
mixGroups=options.mix_groups,
mixReads=options.mix_reads,
interleaved=options.interleave,
bigFile=options.no_gzip,
headersOnly=options.headers_only,
minMapQual=options.mapping_quality,
maxMisMatches=options.max_distance,
useSuppAlignments=options.use_supplementary,
useSecondaryAlignments=options.use_secondary,
verbose=options.verbose,
threads=options.threads)
else:
raise ExtractModeNotAppropriateException("mode: " +
options.mode +
" is unknown")
elif (options.subparser_name == 'merge'):
# make bin cores
print "*******************************************************************************"
print " [[GroopM %s]] Running in bin merging mode..." % self.GMVersion
print "*******************************************************************************"
BM = binManager.BinManager(dbFileName=options.dbname)
BM.loadBins(timer, makeBins=True, silent=False)
BM.merge(options.bids, options.force, saveBins=True)
elif (options.subparser_name == 'split'):
# make bin cores
print "*******************************************************************************"
print " [[GroopM %s]] Running in bin splitting mode..." % self.GMVersion
print "*******************************************************************************"
BM = binManager.BinManager(dbFileName=options.dbname)
BM.loadBins(timer, makeBins=True, silent=False)
BM.split(options.bid,
options.parts,
mode=options.mode,
saveBins=True,
auto=options.force)
elif (options.subparser_name == 'delete'):
# make bin cores
print "*******************************************************************************"
print " [[GroopM %s]] Running in bin deleting mode..." % self.GMVersion
print "*******************************************************************************"
BM = binManager.BinManager(dbFileName=options.dbname)
BM.loadBins(timer, makeBins=True,
silent=True) #, bids=options.bids)
BM.deleteBins(options.bids,
force=options.force,
saveBins=True,
freeBinnedRowIndices=True)
elif (options.subparser_name == 'plot'):
print "*******************************************************************************"
print " [[GroopM %s]] Running in bin plotting mode..." % self.GMVersion
print "*******************************************************************************"
BM = binManager.BinManager(dbFileName=options.dbname)
if options.bids is None:
bids = []
else:
bids = options.bids
BM.loadBins(timer,
makeBins=True,
silent=False,
bids=bids,
loadContigNames=False)
BM.setColorMap(options.cm)
BM.plotBins(FNPrefix=options.tag,
plotEllipsoid=True,
ignoreContigLengths=options.points,
folder=options.folder)
elif (options.subparser_name == 'explore'):
# make bin cores
print "*******************************************************************************"
print " [[GroopM %s]] Running in bin '%s' explorer mode..." % (
self.GMVersion, options.mode)
print "*******************************************************************************"
transform = True ^ options.no_transform
bids = []
if options.bids is not None:
bids = options.bids
BE = groopmUtils.BinExplorer(options.dbname,
bids=bids,
transform=transform,
cmstring=options.cm,
ignoreContigLengths=options.points)
if (options.mode == 'binpoints'):
BE.plotPoints(timer)
elif (options.mode == 'binids'):
BE.plotIds(timer)
elif (options.mode == 'allcontigs'):
BE.plotContigs(timer, coreCut=options.cutoff, all=True)
elif (options.mode == 'unbinnedcontigs'):
BE.plotUnbinned(timer, coreCut=options.cutoff)
elif (options.mode == 'binnedcontigs'):
BE.plotContigs(timer, coreCut=options.cutoff)
elif (options.mode == 'binassignments'):
BE.plotBinAssignents(timer, coreCut=options.cutoff)
elif (options.mode == 'compare'):
BE.plotCompare(timer, coreCut=options.cutoff)
elif (options.mode == 'together'):
BE.plotTogether(timer,
coreCut=options.cutoff,
doMers=options.kmers)
elif (options.mode == 'sidebyside'):
BE.plotSideBySide(timer, coreCut=options.cutoff)
else:
print "**Error: unknown mode:", options.mode
elif (options.subparser_name == 'flyover'):
# make bin cores
print "*******************************************************************************"
print " [[GroopM %s]] Making a flyover..." % self.GMVersion
print "*******************************************************************************"
bids = []
if options.bids is not None:
bids = options.bids
BE = groopmUtils.BinExplorer(options.dbname,
bids=bids,
transform=True,
ignoreContigLengths=options.points)
BE.plotFlyOver(timer,
fps=options.fps,
totalTime=options.totalTime,
percentFade=options.firstFade,
prefix=options.prefix,
showColorbar=options.colorbar,
title=options.title,
coreCut=options.cutoff,
format=options.format)
elif (options.subparser_name == 'highlight'):
# make bin cores
print "*******************************************************************************"
print " [[GroopM %s]] Running in highlighter mode..." % self.GMVersion
print "*******************************************************************************"
bids = []
if options.bids is not None:
bids = options.bids
BE = groopmUtils.BinExplorer(options.dbname,
bids=bids,
binLabelsFile=options.binlabels,
contigColorsFile=options.contigcolors,
ignoreContigLengths=options.points)
BE.plotHighlights(timer,
options.elevation,
options.azimuth,
options.file,
options.filetype,
options.dpi,
drawRadius=options.radius,
show=options.show,
coreCut=options.cutoff,
testing=options.place)
elif (options.subparser_name == 'print'):
BM = binManager.BinManager(dbFileName=options.dbname)
bids = []
if options.bids is not None:
bids = options.bids
BM.loadBins(timer,
getUnbinned=options.unbinned,
makeBins=True,
silent=True,
bids=bids)
BM.printBins(options.format, fileName=options.outfile)
elif (options.subparser_name == 'dump'):
print "*******************************************************************************"
print " [[GroopM %s]] Running in data dumping mode..." % self.GMVersion
print "*******************************************************************************"
# prep fields. Do this first cause users are mot likely to
# mess this part up!
allowable_fields = [
'names', 'mers', 'gc', 'coverage', 'tcoverage', 'ncoverage',
'lengths', 'bins', 'all'
]
fields = options.fields.split(',')
for field in fields:
if field not in allowable_fields:
print "ERROR: field '%s' not recognised. Allowable fields are:" % field
print '\t', ",".join(allowable_fields)
return
if options.separator == '\\t':
separator = '\t'
else:
separator = options.separator
DM = GMDataManager()
DM.dumpData(options.dbname, fields, options.outfile, separator,
not options.no_headers)
return 0
