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fix ValueError: invalid mode: 'rU' with python3.11 #106

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fix ValueError: invalid mode: 'rU' with python3.11 #106

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8 changes: 4 additions & 4 deletions scoary/methods.py
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Original file line number Diff line number Diff line change
Expand Up @@ -181,15 +181,15 @@ def main(**kwargs):
cutoffs.pop(m,None)

# Start analysis
with open(args.genes, "rU") as genes, \
open(args.traits, "rU") as traits:
with open(args.genes, "r") as genes, \
open(args.traits, "r") as traits:

if args.restrict_to is not None:
# Note: Despite being a dictionary, the values of
# allowed_isolates are not currently used, only the keys
allowed_isolates = {isolate : "all"
for line in
open(args.restrict_to,"rU")
open(args.restrict_to,"r")
for isolate in line.rstrip().split(",")}
else:
# Despite the confusing name
Expand Down Expand Up @@ -343,7 +343,7 @@ def Csv_to_dic_Roary(genefile, delimiter, grabcols, startcol=14,

if writereducedset:
file = open(ReduceSet(genefile,delimiter, grabcols, startcol,
allowed_isolates,time,outdir),"rU")
allowed_isolates,time,outdir),"r")
csvfile = csv.reader(file, skipinitialspace=True,
delimiter=delimiter)
else:
Expand Down
2 changes: 1 addition & 1 deletion scoary/vcf2scoary.py
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Original file line number Diff line number Diff line change
Expand Up @@ -100,7 +100,7 @@ def main():
if not os.path.isfile(args.vcf):
sys.exit("Unable to locate input file %s" % args.vcf)

with open(args.vcf,'rU') as vcffile, open(args.out,'w') as outfile:
with open(args.vcf,'r') as vcffile, open(args.out,'w') as outfile:
lines = csv.reader(vcffile, delimiter='\t', quotechar='"')
metainfo = {"##INFO" : {},
"##FILTER" : {},
Expand Down
4 changes: 2 additions & 2 deletions tests/test_scoary_output.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@


for Test in ["1","2","4"]:
with open(os.getcwd() + "/Test" + Test + "/Tetracycline_resistance.results.csv" ,"rU") as resfile:
with open(os.getcwd() + "/Test" + Test + "/Tetracycline_resistance.results.csv" ,"r") as resfile:
tab = csv.reader(resfile, delimiter=",")
for i in range(2):
if i == 0:
Expand Down Expand Up @@ -120,7 +120,7 @@
print("Not equal at Test %s col 17: %s %s" % (Test, data[17], str(reference[17])))
sys.exit(-1)

with open(os.getcwd() + "/mutations_presence_absence.csv" ,"rU") as vcfresfile:
with open(os.getcwd() + "/mutations_presence_absence.csv" ,"r") as vcfresfile:
tab = csv.reader(vcfresfile, delimiter=",")
for i in range(2):
if i == 0:
Expand Down