From 3605eb72c6eaadd8818e6250eafb5f9e3ec4a366 Mon Sep 17 00:00:00 2001
From: remy <remy.dernat@umontpellier.fr>
Date: Fri, 29 Nov 2019 12:21:23 +0100
Subject: [PATCH] jSpeciesOpen is not needed as it is the same as iSpeciesOpen
---
orthofinder/scripts/blast_file_processor.py | 2 +-
orthofinder/scripts/scnorm.py | 8 ++++----
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/orthofinder/scripts/blast_file_processor.py b/orthofinder/scripts/blast_file_processor.py
index 72a6952..80f9eaf 100644
--- a/orthofinder/scripts/blast_file_processor.py
+++ b/orthofinder/scripts/blast_file_processor.py
@@ -153,7 +153,7 @@ def WriteFixNormalizedBlastFile(blastDir_list, iSpecies, jSpecies, sep = "_", qD
blastwriter = csv.writer(tempfile, delimiter='\t')
for row in blastreader:
rows.append(row)
- newrows = sc.scnorm.FixZeroNormalizedScores(iSpeciesOpen, jSpeciesOpen, rows)
+ newrows = sc.scnorm.FixZeroNormalizedScores(iSpeciesOpen, rows)
for the_row in newrows:
blastwriter.writerow(the_row)
tempfile.flush()
diff --git a/orthofinder/scripts/scnorm.py b/orthofinder/scripts/scnorm.py
index ed9cc2f..2f656bc 100644
--- a/orthofinder/scripts/scnorm.py
+++ b/orthofinder/scripts/scnorm.py
@@ -148,7 +148,7 @@ class scnorm:
return newrows
@staticmethod
- def FixZeroNormalizedScores(iSpeciesOpen, jSpeciesOpen, rows):
+ def FixZeroNormalizedScores(iSpeciesOpen, rows):
"""
This function retrieve the Normalization Score
from current csv file (with Seq iQ, Seq iH)
@@ -159,10 +159,10 @@ class scnorm:
NormBS = selfHitNormBlastScore
newrows = []
# retrieve value from plot https://code-examples.net/en/q/8863d1
- all_plots = f[jSpeciesOpen][0].get_xydata()
+ all_plots = f[iSpeciesOpen][0].get_xydata()
error_margin = 0.2
#line = 0
- print("Compute back 0.0 normalized score for self-hits for species %d %d" % (iSpeciesOpen, jSpeciesOpen))
+ print("Compute back 0.0 normalized score for self-hits for species %d %d" % (iSpeciesOpen, iSpeciesOpen))
print("Error margin is %f" % error_margin)
for row in rows:
#try:
@@ -177,7 +177,7 @@ class scnorm:
#except (IndexError, ValueError):
# sys.stderr.write("\nERROR: 12th field in BLAST results file line should be the bit-score for the hit\n")
#except IndexError as e:
- # sys.stderr.write("\nERROR: csv values on Blast species %d %d file, line %d : %s \n" % (iSpeciesOpen, jSpeciesOpen, line, e))
+ # sys.stderr.write("\nERROR: csv values on Blast species %d %d file, line %d : %s \n" % (iSpeciesOpen, iSpeciesOpen, line, e))
# pass
newrows.append(row)
#line+=1
--
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