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ca5a371
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use the compression handling auto-opener for our eland files
author
Diane Trout
<diane@caltech.edu>
Fri, 13 Feb 2009 01:42:06 +0000
(
01:42
+0000)
committer
Diane Trout
<diane@caltech.edu>
Fri, 13 Feb 2009 01:42:06 +0000
(
01:42
+0000)
scripts/makebed
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diff --git
a/scripts/makebed
b/scripts/makebed
index 64ba518b1a91e54812938dce8fb813a51e38bf93..577b86891f098ab5c7cfeb6e2b4139814f1731a5 100755
(executable)
--- a/
scripts/makebed
+++ b/
scripts/makebed
@@
-3,6
+3,7
@@
import optparse
import sys
import os
import sys
import os
+from htsworkflow.util.opener import autoopen
from htsworkflow.util.makebed import make_bed_from_eland_stream, make_bed_from_multi_eland_stream, make_description
def make_parser():
from htsworkflow.util.makebed import make_bed_from_eland_stream, make_bed_from_multi_eland_stream, make_description
def make_parser():
@@
-61,7
+62,7
@@
def main(command_line=None):
if options.inname == '-':
instream = sys.stdin
elif os.path.exists(options.inname):
if options.inname == '-':
instream = sys.stdin
elif os.path.exists(options.inname):
- instream = open(options.inname, 'r')
+ instream =
auto
open(options.inname, 'r')
else:
parser.error('%s was not found' % (options.inname))
return 1
else:
parser.error('%s was not found' % (options.inname))
return 1