def run(self): if self.saveInter is not True: bamPath = os.path.join(self.getLocalTempDir(), self.uuid + ".bam") fastqPath = os.path.join(self.getLocalTempDir(), self.uuid + ".fastq") else: bamPath = os.path.join(self.outDir, self.uuid + ".bam") fastqPath = os.path.join(self.outDir, self.uuid + ".fastq") models.downloadQuery(fastqPath, self.getLocalTempDir(), self.key, self.queryString, self.uuid) models.alignQuery(fastqPath, bamPath, self.getLocalTempDir(), self.uuid, self.index) sun = models.FilteredSunModel(self.outDir, self.uuid, bamPath) sun.run() unfilteredSun = models.UnfilteredSunModel(self.outDir, self.uuid, bamPath) unfilteredSun.run() ilp = models.IlpModel(self.outDir, self.bpPenalty, self.dataPenalty, self.tightness, fastqPath, self.uuid, self.graph, self.getLocalTempDir(), self.kmerSize, self.saveInter, sun.C, sun.D) ilp.run() models.combinedPlot(ilp.resultDict, ilp.rawCounts, ilp.offsetMap, unfilteredSun.hg38ResultDict, self.uuid, self.outDir)
def run(self): if self.saveInter is not True: bamPath = os.path.join(self.getLocalTempDir(), self.uuid + ".bam") else: bamPath = os.path.join(self.outDir, self.uuid + ".bam") if not os.path.exists(bamPath): models.alignQuery(self.fastqPath, bamPath, self.getLocalTempDir(), self.uuid, self.index) sun = models.FilteredSunModel(self.outDir, self.uuid, bamPath, doIlp=True) sun.run() unfilteredSun = models.UnfilteredSunModel(self.outDir, self.uuid, bamPath, doIlp=True) unfilteredSun.run()
def run(self): if self.saveInter is not True: bamPath = os.path.join(self.getLocalTempDir(), self.uuid + ".bam") else: bamPath = os.path.join(self.outDir, self.uuid + ".bam") models.alignQuery(self.fastqPath, bamPath, self.getLocalTempDir(), self.uuid, self.index) sun = models.FilteredSunModel(self.outDir, self.uuid, bamPath) sun.run() unfilteredSun = models.UnfilteredSunModel(self.outDir, self.uuid, bamPath) unfilteredSun.run() ilp = models.IlpModel(self.outDir, self.bpPenalty, self.dataPenalty, self.tightness, self.fastqPath, self.uuid, self.graph, self.getLocalTempDir(), saveInter) ilp.run() models.combinedPlot(ilp.resultDict, ilp.offsetMap, sun.resultDict, unfilteredSun.resultDict, self.uuid, self.outDir)
def run(self): fastqPath = os.path.join(self.outDir, self.uuid + ".fastq") if not os.path.exists(fastqPath): raise RuntimeError("fastq not in fastqPath. Schema is <uuid>.fastq. uuid: {}".format(self.uuid)) if self.saveInter is not True: bamPath = os.path.join(self.getLocalTempDir(), self.uuid + ".bam") else: bamPath = os.path.join(self.outDir, self.uuid + ".bam") if not os.path.exists(bamPath): models.alignQuery(fastqPath, bamPath, self.getLocalTempDir(), self.uuid, self.index) sun = models.FilteredSunModel(self.outDir, self.uuid, bamPath) sun.run() unfilteredSun = models.UnfilteredSunModel(self.outDir, self.uuid, bamPath) unfilteredSun.run() ilp = models.IlpModel(self.outDir, self.bpPenalty, self.dataPenalty, self.tightness, fastqPath, self.uuid, self.graph, self.getLocalTempDir(), self.kmerSize, self.saveInter, sun.C, sun.D) ilp.run() models.combinedPlot(ilp.resultDict, ilp.rawCounts, ilp.offsetMap, unfilteredSun.hg38ResultDict, self.uuid, self.outDir)