From 1471cfc7569e31361530bfd56de7393da73de28e Mon Sep 17 00:00:00 2001
From: remy <remy.dernat@umontpellier.fr>
Date: Sun, 24 Nov 2019 18:41:52 +0100
Subject: [PATCH] not the right way to do fix this
---
orthofinder/scripts/blast_file_processor.py | 5 +++--
orthofinder/scripts/scnorm.py | 25 +++++++++++----------
2 files changed, 16 insertions(+), 14 deletions(-)
diff --git a/orthofinder/scripts/blast_file_processor.py b/orthofinder/scripts/blast_file_processor.py
index be32ead..a22ad19 100644
--- a/orthofinder/scripts/blast_file_processor.py
+++ b/orthofinder/scripts/blast_file_processor.py
@@ -34,6 +34,7 @@ from . import util
from . import matrices
from tempfile import NamedTemporaryFile
from shutil import move
+from . import scnorm as sc
PY2 = sys.version_info <= (3,)
file_read_mode = 'rb' if PY2 else 'rt'
@@ -140,8 +141,8 @@ def WriteNormalizedBlastFile(blastDir_list, B, iSpecies, jSpecies, sep = "_", qD
raise
try:
newscore = B[sequence1ID, sequence2ID]
- #if newscore == "0.0":
- # FixZeroNormScore(int(row[12]))
+ #if newscore == 0.0:
+ # 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 d28a4ef..1f60037 100644
--- a/orthofinder/scripts/scnorm.py
+++ b/orthofinder/scripts/scnorm.py
@@ -34,6 +34,7 @@ import matplotlib.pyplot as plt # install
counter=0
+curvefitplt=[]
"""
scnorm
@@ -85,7 +86,7 @@ class scnorm:
# curve_fit doc.: https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.curve_fit.html
Slog = np.log10(S)
pars, covar = curve_fit(scnorm.loglinear, Lf, Slog)
- scnorm.DrawLogLinear(pars, Lf, Slog)
+ scnorm.DrawLogLinear(pars, Lf)
return pars
@staticmethod
@@ -101,24 +102,24 @@ class scnorm:
return sparse.lil_matrix(10**(-params[1]) * li_matrix * b * lj_matrix)
@staticmethod
- def DrawLogLinear(params, x, y):
+ def DrawLogLinear(params, x):
+ global counter
+ global curvefitplt
nbvals=5000
maxBS=2500
minBS=0
x = np.linspace(minBS, maxBS, nbvals)
- 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('Normalized Scores')
- plt.ylabel('Bits Scores')
- plt.title("Normalisation fitting curve for species")
+ plt.xlabel('Bits Scores')
+ plt.ylabel('Normalized Scores')
+ plt.title("Normalization fitting curve for species")
plt.grid(True)
- #plt.savefig('foo'+str(counter)+'.png')
plt.savefig('fitting_curve.png')
- global counter
counter+=1
@staticmethod
- def FixZerosNormalizedBS(x):
- Xlog=log10(x)
- return Xlog
- #return NBS
+ def FixZeroNormalizedScores(species, x):
+ NormBS = curvefitplt[species][int(x)].get_data()
+ return NormBS
--
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