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")
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):
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)
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)
