diff --git a/orthofinder/orthofinder.py b/orthofinder/orthofinder.py index 2694d6f4e85e285aeb459f1b19c1379c0006984a..50b2e80632e9abef78790f4a16f3919b6686951a 100755 --- a/orthofinder/orthofinder.py +++ b/orthofinder/orthofinder.py @@ -501,7 +501,8 @@ class WaterfallMethod: Bij = blast_file_processor.GetBLAST6Scores(seqsInfo, blastDir_list, seqsInfo.speciesToUse[iSpecies], seqsInfo.speciesToUse[jSpecies], qDoubleBlast=qDoubleBlast) Bij = WaterfallMethod.NormaliseScores(Bij, Lengths, iSpecies, jSpecies) if qNormalize: - WaterfallMethod.WriteNewScores(seqsInfo, blastDir_list, Bij, iSpecies, qDoubleBlast=qDoubleBlast) + #WaterfallMethod.WriteNewScores(seqsInfo, blastDir_list, Bij, iSpecies, qDoubleBlast=qDoubleBlast) + WaterfallMethod.WriteNewScores(seqsInfo, blastDir_list, Bij, seqsInfo.speciesToUse[iSpecies], qDoubleBlast=qDoubleBlast) Bi.append(Bij) matrices.DumpMatrixArray("B", Bi, iSpecies) BH = GetBH_s(Bi, seqsInfo, iSpecies) @@ -867,7 +868,8 @@ def PrintHelp(prog_caller): print("") print("WORKFLOW RESTART COMMANDS:") - print(" -b <dir> Start OrthoFinder from pre-computed BLAST results in <dir>") + print(" -b <dir> Start OrthoFinder from pre-computed BLAST results in <dir>") + print(" -N <dir> Normalize Blast scores from pre-computed BLAST results in <dir>, then exit") print(" -fg <dir> Start OrthoFinder from pre-computed orthogroups in <dir>") print(" -ft <dir> Start OrthoFinder from pre-computed gene trees in <dir>") @@ -950,7 +952,7 @@ def ProcessArgs(prog_caller): Start from: -f: 1,2,..,6 (start from fasta files, --fasta) -b: 4,5,6 (start from blast results, --blast) - -N: 3.b (start from blast results, --normalize) + -N: 3.b (start from blast results, --normalize) -fg: 5,6 (start from orthogroups/do orthologue workflow, --from-groups) -ft: 6 (start from gene tree/do reconciliation, --from-trees) Stop at: