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allow RM2Bed to read and write from pipes #253

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allow RM2Bed to read and write from pipes #253

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8 changes: 5 additions & 3 deletions util/RM2Bed.py
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Original file line number Diff line number Diff line change
Expand Up @@ -203,6 +203,8 @@ def openOptGzipFile(filename, modes='r'):
Returns:
A file object
"""
if filename == "-":
return sys.stdin
f = open(filename, 'b'+modes)
# First two byte signature of a gzip'd file
if (f.read(2) == b'\x1f\x8b'):
Expand Down Expand Up @@ -437,7 +439,7 @@ def __call__(self, parser, args, values, option_string=None):

LOGGER.info("#\n# RM2Bed.py\n#")

if ( not os.path.exists(args.rm_file) ):
if args.rm_file != '-' and ( not os.path.exists(args.rm_file) ):
raise Exception("File " + args.rm_file + " is missing.")
LOGGER.info("Data File: " + args.rm_file)

Expand Down Expand Up @@ -770,12 +772,12 @@ def __call__(self, parser, args, values, option_string=None):

# Write as monolithic file
if args.output_bed == '-':
output_bed = "/dev/stdout"
output_bed = sys.stdout
elif args.output_bed is not None:
output_bed = args.output_bed
else:
output_bed = file_prefix + '_rm.bed'
LOGGER.info("Creating: " + output_bed)
LOGGER.info("Creating: " + str(output_bed))
annot_dataframe.to_csv(output_bed, sep='\t', header=False, index=False)

#
Expand Down