From c2e2a5fd06402e8d3f3e90a5cf277db91fe84507 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dernat?= <remy.dernat@umontpellier.fr>
Date: Tue, 12 Nov 2019 11:24:49 +0100
Subject: [PATCH] check ipsecies
---
orthofinder/orthofinder.py | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/orthofinder/orthofinder.py b/orthofinder/orthofinder.py
index 2694d6f..50b2e80 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:
--
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