diff --git a/orthofinder/scripts/blast_file_processor.py b/orthofinder/scripts/blast_file_processor.py index 72a6952df035760e0ffa03c524248860b24ffb7d..80f9eafc9ff5d29fd9ed9f452e7d481ff40c753c 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 ed9cc2f3c4be234742033d8e44c70987a9121d3e..2f656bc4e89d1969efc242db0bb265a6f872c4d3 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