From 1a4c63040ee32e9b0b287b2d0828af1ffbc44763 Mon Sep 17 00:00:00 2001
From: remy <remy.dernat@umontpellier.fr>
Date: Tue, 26 Nov 2019 10:03:21 +0100
Subject: [PATCH] remove non necessary code
---
orthofinder/scripts/blast_file_processor.py | 2 --
orthofinder/scripts/scnorm.py | 6 ------
2 files changed, 8 deletions(-)
diff --git a/orthofinder/scripts/blast_file_processor.py b/orthofinder/scripts/blast_file_processor.py
index 3627c29..01ff53e 100644
--- a/orthofinder/scripts/blast_file_processor.py
+++ b/orthofinder/scripts/blast_file_processor.py
@@ -143,8 +143,6 @@ def WriteNormalizedBlastFile(blastDir_list, B, iSpecies, jSpecies, sep = "_", qD
newscore = B[sequence1ID, sequence2ID]
if newscore == 0.0:
sys.stderr.write("\nERROR: 0.0 value detected in seq position %d %d for Blast species %d %d!\n" % (sequence1ID, sequence2ID, iSpeciesOpen, jSpeciesOpen))
-
- # newscore = sc.scnorm.FixZeroNormalizedScores(iSpeciesOpen, float(row[11]))
row.append(newscore)
except IndexError as e:
sys.stderr.write("\nERROR: Matrix index on Blast species %d %d, sequences B[%d, %d] : %s \n" % (iSpeciesOpen, jSpeciesOpen, sequence1ID, sequence2ID, e))
diff --git a/orthofinder/scripts/scnorm.py b/orthofinder/scripts/scnorm.py
index b6b041b..4cc47b5 100644
--- a/orthofinder/scripts/scnorm.py
+++ b/orthofinder/scripts/scnorm.py
@@ -119,9 +119,3 @@ class scnorm:
plt.grid(True)
plt.savefig('fitting_curve.png')
counter+=1
-
- #@staticmethod
- #def FixZeroNormalizedScores(species, x):
- # https://code-examples.net/en/q/8863d1
- #NormBS = curvefitplt[species][int(x)].get_data()
- #return NormBS
--
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