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Python 3: use "as" instead of comma in except clause

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This commit is contained in:
Nicola Soranzo
2016-05-17 23:53:16 +01:00
parent ed4132d9c0
commit 8a43b2b492
73 changed files with 152 additions and 152 deletions
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scripts/microbes/harvest_bacteria.py
+3 -3
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@@ -170,7 +170,7 @@ def process_Genbank( filename, org_num, refseq ):
def process_Glimmer3( filename, org_num, refseq ):
try:
glimmer3_bed = get_bed_from_glimmer3( filename, refseq )
except Exception, e:
except Exception as e:
print "Converting Glimmer3 to bed FAILED! For chrom:", refseq, "file:", filename, e
glimmer3_bed = []
glimmer3_bed_file = open( os.path.join( os.path.split( filename )[0], "%s.Glimmer3.bed" % refseq ), 'wb+' )
@@ -181,7 +181,7 @@ def process_Glimmer3( filename, org_num, refseq ):
def process_GeneMarkHMM( filename, org_num, refseq ):
try:
geneMarkHMM_bed = get_bed_from_GeneMarkHMM( filename, refseq )
except Exception, e:
except Exception as e:
print "Converting GeneMarkHMM to bed FAILED! For chrom:", refseq, "file:", filename, e
geneMarkHMM_bed = []
geneMarkHMM_bed_bed_file = open( os.path.join( os.path.split( filename )[0], "%s.GeneMarkHMM.bed" % refseq ), 'wb+' )
@@ -192,7 +192,7 @@ def process_GeneMarkHMM( filename, org_num, refseq ):
def process_GeneMark( filename, org_num, refseq ):
try:
geneMark_bed = get_bed_from_GeneMark( filename, refseq )
except Exception, e:
except Exception as e:
print "Converting GeneMark to bed FAILED! For chrom:", refseq, "file:", filename, e
geneMark_bed = []
geneMark_bed_bed_file = open( os.path.join( os.path.split( filename )[0], "%s.GeneMark.bed" % refseq ), 'wb+' )