Merge branch 'master' of gitosis@mus.cacr.caltech.edu:htsworkflow

[htsworkflow.git] / scripts / elandseq

diff --git a/scripts/elandseq b/scripts/elandseq
deleted file mode 100755 (executable)
index 6a5178c..0000000
--- a/scripts/elandseq
+++ /dev/null
@@ -1,51 +0,0 @@
-#!/usr/bin/env python
-import optparse
-import os
-import sys
-
-from htsworkflow.pipelines.eland import extract_eland_sequence
-
-def make_parser():
-  usage = "usage: %prog [options] infile [outfile]"
-
-  parser = optparse.OptionParser(usage)
-  parser.add_option("-e", "--extract", dest="slice",
-    default=":",
-    help="provide a python slice operator to select a portion of an eland file")
-  return parser
-
-def main(argv):
-  parser = make_parser()
-
-  (opt, args) = parser.parse_args(argv)
-
-  if len(args) not in (0, 1, 2):
-    parser.error('incorrect number of arguments')
-
-  # get our slice coordinates
-  start, end = opt.slice.split(':')
-  if len(start) > 0:
-    start = int(start)
-  else:
-    start = None
-  if len(end) > 0:
-    end = int(end)
-  else:
-    end = None
-
-  # open infile
-  if len(args) > 0:
-    instream = open(args[0],'r')
-  else:
-    instream = sys.stdin
-
-  if len(args) > 1:
-    outstream = open(args[1],'w')
-  else:
-    outstream = sys.stdout
-
-  extract_eland_sequence(instream, outstream, start, end)
-
-if __name__ == "__main__":
-    sys.exit(main(sys.argv[1:]))
-