diff --git a/ngsphy/readcounts.py b/ngsphy/readcounts.py index f92f824..19fea08 100644 --- a/ngsphy/readcounts.py +++ b/ngsphy/readcounts.py @@ -1424,16 +1424,26 @@ def launchCommand(self, referenceForCurrST, indexREP,indexLOC, individuals,cover nLoci=self.numLociPerReplicate[indexREP-1] self.appLogger.debug("Iterating over nLoci: {0}/{1}".format(indexLOC,nLoci)) numGeneTreeDigits=len(str(nLoci)) - filepathLoc=os.path.join(\ - self.settings.basepath,\ - "{0:0{1}d}".format(indexREP,self.numReplicatesDigits),\ - "{0}_{1:0{2}d}_TRUE.fasta".format(\ - self.settings.simphyDataPrefix,\ - indexLOC,\ - numGeneTreeDigits\ - )\ - ) - + if self.settings.inputmode<4: + filepathLoc=os.path.join(\ + self.settings.basepath,\ + "REPLICATE_{0:0{1}d}".format(indexREP,self.numReplicatesDigits),\ + "{0}_{1:0{2}d}_TRUE.fasta".format(\ + self.settings.simphyDataPrefix,\ + indexLOC,\ + numGeneTreeDigits\ + )\ + ) + else: + filepathLoc=os.path.join(\ + self.settings.basepath,\ + "{0:0{1}d}".format(indexREP,self.numReplicatesDigits),\ + "{0}_{1:0{2}d}_TRUE.fasta".format(\ + self.settings.simphyDataPrefix,\ + indexLOC,\ + numGeneTreeDigits\ + )\ + ) # dictionary. indices=variable sites, content=variable nucleotide set self.appLogger.debug(\ "Extracting variable positions from Replicate - {0:0{1}d}/ Locus - {2:0{3}d}".format(\