From ea3105bb15eaf94f79016435bdfdcb8c5b82a7f2 Mon Sep 17 00:00:00 2001
From: remy <remy.dernat@umontpellier.fr>
Date: Sun, 24 Nov 2019 19:12:13 +0100
Subject: [PATCH] 0.0 ...
---
orthofinder/scripts/blast_file_processor.py | 4 +++-
orthofinder/scripts/scnorm.py | 18 ++++++++++--------
2 files changed, 13 insertions(+), 9 deletions(-)
diff --git a/orthofinder/scripts/blast_file_processor.py b/orthofinder/scripts/blast_file_processor.py
index a22ad19..fea78cb 100644
--- a/orthofinder/scripts/blast_file_processor.py
+++ b/orthofinder/scripts/blast_file_processor.py
@@ -141,7 +141,9 @@ def WriteNormalizedBlastFile(blastDir_list, B, iSpecies, jSpecies, sep = "_", qD
raise
try:
newscore = B[sequence1ID, sequence2ID]
- #if newscore == 0.0:
+ if newscore == 0.0:
+ sys.stderr.write("\nERROR: 0.0 value detected !\n")
+
# newscore = sc.scnorm.FixZeroNormalizedScores(iSpeciesOpen, float(row[11]))
row.append(newscore)
except IndexError as e:
diff --git a/orthofinder/scripts/scnorm.py b/orthofinder/scripts/scnorm.py
index 1f60037..b6b041b 100644
--- a/orthofinder/scripts/scnorm.py
+++ b/orthofinder/scripts/scnorm.py
@@ -34,7 +34,7 @@ import matplotlib.pyplot as plt # install
counter=0
-curvefitplt=[]
+#curvefitplt=[]
"""
scnorm
@@ -104,13 +104,14 @@ class scnorm:
@staticmethod
def DrawLogLinear(params, x):
global counter
- global curvefitplt
+ #global curvefitplt
nbvals=5000
maxBS=2500
minBS=0
x = np.linspace(minBS, maxBS, nbvals)
- plot = plt.plot(x, scnorm.loglinear(x, *params), label='species '+str(counter))
- curvefitplt.append(plot)
+ plt.plot(x, scnorm.loglinear(x, *params), label='species '+str(counter))
+ #plot = plt.plot(x, scnorm.loglinear(x, *params), label='species '+str(counter))
+ #curvefitplt.append(plot)
plt.legend()
plt.xlabel('Bits Scores')
plt.ylabel('Normalized Scores')
@@ -119,7 +120,8 @@ class scnorm:
plt.savefig('fitting_curve.png')
counter+=1
- @staticmethod
- def FixZeroNormalizedScores(species, x):
- NormBS = curvefitplt[species][int(x)].get_data()
- return NormBS
+ #@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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