def preprocess(self, lib):
"""
The method preprocess determines which preprocessing steps have to be executed for a given library.
"""
logging.info("Preprocessing of " + lib.libName)
LaTeX.ltxSection("Preprocessing of " + lib.libName)
lib.forward = DirUtils.fileRegexToList(lib.forward)
lib.reversed = DirUtils.fileRegexToList(lib.reversed)
if lib.format == "sff":
for idx, sffFile in enumerate(lib.forward):
lib.forward[idx] = SffToFastqConverter.SffToFastqConverter(lib.outputDir, sffFile=sffFile).execute()
smallReport = FastqSmallReport.FastqSmallReport()
smallReport.createSmallReport(lib.forward, lib.reversed)
if len(lib.forward) > 1:
lib.forward = FastqCommands.MergeCommand(lib.outputDir, direction="forward", fastqFiles=lib.forward).execute()
if lib.reversed != None:
lib.reversed = FastqCommands.MergeCommand(lib.outputDir, direction="reversed", fastqFiles=lib.forward).execute()
FastqSmallReport.FastqSmallReport().createSmallReport(lib.forward, lib.reversed)
else:
lib.forward = lib.forward[0]
if lib.reversed != None:
lib.reversed = lib.reversed[0]
lib.avgReadlength = float(smallReport.fastqInfo[smallReport.fastqInfo.keys()[0]][2])
if lib.sequencingPlatform == "illumina":
self.illuminaPreprocess(lib)
elif lib.sequencingPlatform == "454":
lib.forward = FastqMcfTrimming.FastqTrimmer(lib.outputDir, forward=lib.forward,noTrim=True).execute()
FastqSmallReport.FastqSmallReport().createSmallReport(lib.forward, lib.reversed)
self.filterContamination(lib)
def doAssembly(self, pool):
"""
The method doAssembly creates all objects to execute a wgs assembly. Afterwards the insert sizes of all pe and
mp libraries are estimated.
"""
logging.info("Executing assembly")
LaTeX.ltxSection("Assembly")
if Configuration.instance.getGlobalOption("assembler") == None or Configuration.instance.getGlobalOption("assembler") == "wgs":
assembler = WgsAssembler.WgsAssembler()
self.assembly = assembler.doAssembly(pool.outputDir + "assembly/", pool)
elif Configuration.instance.getGlobalOption("assembler") == "allpaths":
self.assembly = AllpathsAssembler.AllpathsAssembler().doAssembly(pool.outputDir + "allPathsAssembly/", pool)
for lib in pool.libs:
if lib.reversed == None:
continue
logging.info("Calculating insert sizes for " + lib.libName)
insertSizeChecker = InsertSizeChecker.InsertSizeChecker()
insertSizeChecker.checkInsertSize(lib.outputDir, lib.rawForward, lib.rawReversed, self.assembly, lib.libName, lib.insertSize)
def doGenomeSizeEstimation(self, outputDir, pool):
"""
The method doGenomeSizeEstimation contains the mainflow of the genomesize estimation. This mainflow contains the following methods:
* Execute Jellyfish count
* Execute Jellyfish stats
* Create a histogram of the unique kmers with Jellyfish histo
* Draw a histogram of the unique kmers
* Estimate the genome size with the BGI method
"""
logging.info("Starting genome size estimation")
if not os.path.isdir(outputDir):
os.makedirs(outputDir)
LaTeX.ltxSection("Genome size estimation}")
self.jellyFishCountsFile = JellyFish.JellyFishCount(outputDir, pool=pool).execute()
self.jellyFishStatsFile = JellyFish.JellyFishStats(outputDir, jellyFishCountsFile=self.jellyFishCountsFile).execute()
self.jellyfishHistoFile = JellyFish.JellyFishHisto(outputDir, jellyFishCountsFile=self.jellyFishCountsFile).execute()
self.genSizeHistoPlot = outputDir + "kmer_graph.png"
self.peak = int(self.drawHisto(self.jellyfishHistoFile, self.genSizeHistoPlot))
self.calculateGenomeSize(pool, self.jellyFishStatsFile, self.jellyfishHistoFile)
Reporter.instance.objects.append(self)