def loadEnvData(self):
def _hdrPreProc(row):
ind = row.index("Latitude, Longitute (DD)")
assert ind == 3
return [ re.sub(r"[^a-zA-Z0-9_]+","_",name).strip("_") for name in (["id_samp"]+row[1:ind]+["Latitude (DD)", "Longitute (DD)"]+row[ind+1:]) ]
def _preProc(row,*l,**kw):
ind = 3
return (row[:ind]+row[ind].split(",")+row[ind+1:],)
PostPredAn.loadEnvData(csvInp=self.envInpCsv,dbOut=self.dbMergeFile,preProc=_preProc,hdrPreProc=_hdrPreProc)
def merge(self):
samples = [ (sampSubDir.split("_")[0],pjoin(self.topPredDir,sampSubDir,"results/pred-taxa.sqlite")) for \
sampSubDir in self.sampSubDirs ]
PostPredAn.mergeStats(samples=samples,dbOut=self.dbMergeFile)
def exportPivots(self):
makedir(self.topPivotDir)
PostPredAn.exportAsPivots(dbInp=self.dbMergeFile,csvOutBase=self.csvPivotBase,minWeight=100)
def exportEnvData(self):
makedir(self.topEnvDir)
PostPredAn.exportEnvData(dbInp=self.dbMergeFile,csvOutBase=self.csvEnvBase)
