diff --git a/orthofinder/orthofinder.py b/orthofinder/orthofinder.py index 50b2e80632e9abef78790f4a16f3919b6686951a..2a988970a0a196e157e04e7530fa3c020ca0235d 100755 --- a/orthofinder/orthofinder.py +++ b/orthofinder/orthofinder.py @@ -502,7 +502,7 @@ class WaterfallMethod: Bij = WaterfallMethod.NormaliseScores(Bij, Lengths, iSpecies, jSpecies) if qNormalize: #WaterfallMethod.WriteNewScores(seqsInfo, blastDir_list, Bij, iSpecies, qDoubleBlast=qDoubleBlast) - WaterfallMethod.WriteNewScores(seqsInfo, blastDir_list, Bij, seqsInfo.speciesToUse[iSpecies], qDoubleBlast=qDoubleBlast) + WaterfallMethod.WriteNewScores(seqsInfo, blastDir_list, Bij, seqsInfo.speciesToUse[iSpecies], seqsInfo.speciesToUse[jSpecies], qDoubleBlast=qDoubleBlast) Bi.append(Bij) matrices.DumpMatrixArray("B", Bi, iSpecies) BH = GetBH_s(Bi, seqsInfo, iSpecies) @@ -519,12 +519,11 @@ class WaterfallMethod: return @staticmethod - def WriteNewScores(seqsInfo, blastDir_list, B, iSpecies, qDoubleBlast): + def WriteNewScores(seqsInfo, blastDir_list, B, iSpecies, jScpecies, qDoubleBlast): with warnings.catch_warnings(): warnings.simplefilter("ignore") # process up to the best hits for each species; Bi is a list of matrices - for jSpecies in range(seqsInfo.nSpecies): - blast_file_processor.WriteNormalizedBlastFile(blastDir_list, B, seqsInfo.speciesToUse[iSpecies], seqsInfo.speciesToUse[jSpecies], qDoubleBlast=qDoubleBlast) + blast_file_processor.WriteNormalizedBlastFile(blastDir_list, B, iSpecies, jSpecies, qDoubleBlast=qDoubleBlast) @staticmethod def ConnectCognates(seqsInfo, iSpecies):