From 2bfe970599b185a64a2675eef4df8aa3de6c9043 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dernat?= <remy.dernat@umontpellier.fr>
Date: Tue, 12 Nov 2019 09:27:35 +0100
Subject: [PATCH] renaming a function
---
orthofinder/scripts/blast_file_processor.py | 2 +-
orthofinder/scripts/matrices.py | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/orthofinder/scripts/blast_file_processor.py b/orthofinder/scripts/blast_file_processor.py
index 6e77c47..de669e0 100644
--- a/orthofinder/scripts/blast_file_processor.py
+++ b/orthofinder/scripts/blast_file_processor.py
@@ -119,7 +119,7 @@ def WriteNormalizedBlastFile(blastDir_list, B, iSpecies, jSpecies, sep = "_", qD
iH = 1
iSpeciesOpen = iSpecies
jSpeciesOpen = jSpecies
- #xSeqID, ySeqID, NormVal = ParseMatrix(B)
+ #xSeqID, ySeqID, NormVal = ListFromMatrix(B)
row = ""
for d in blastDir_list:
fn = d + "Blast%d_%d.txt" % (iSpeciesOpen, jSpeciesOpen)
diff --git a/orthofinder/scripts/matrices.py b/orthofinder/scripts/matrices.py
index 11c0bb7..1111fb0 100644
--- a/orthofinder/scripts/matrices.py
+++ b/orthofinder/scripts/matrices.py
@@ -77,7 +77,7 @@ def sparse_max_row(csr_mat):
ret[np.diff(csr_mat.indptr) != 0] = np.maximum.reduceat(csr_mat.data,csr_mat.indptr[:-1][np.diff(csr_mat.indptr)>0])
return ret
-def ParseMatrix(mat):
+def ListsFromMatrix(mat):
bdok = mat.todok()
SortedMat = sorted(bdok.items())
NormVal=[]
@@ -90,4 +90,4 @@ def ParseMatrix(mat):
NormVal.append(SortedMat[i][1])
#for i in range(len(Nval)):
# print("iSpeciesID_%i\tjSpeciesID_%i ... %f" % (xSeqID[i], ySeqID[i], NormVal[i]))
- return xSeqID, ySeqID, NormVal
\ No newline at end of file
+ return xSeqID, ySeqID, NormVal
--
GitLab