From 02cc68e3a277fa117554325c0b764e1dc865797e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dernat?= <remy.dernat@umontpellier.fr>
Date: Tue, 12 Nov 2019 11:37:13 +0100
Subject: [PATCH] error in index
---
orthofinder/orthofinder.py | 7 +++----
1 file changed, 3 insertions(+), 4 deletions(-)
diff --git a/orthofinder/orthofinder.py b/orthofinder/orthofinder.py
index 50b2e80..2a98897 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):
--
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