Rename all the scripts to start with htsw-

[htsworkflow.git] / scripts / makebed

diff --git a/scripts/makebed b/scripts/makebed
deleted file mode 100755 (executable)
index 577b868..0000000
--- a/scripts/makebed
+++ /dev/null
@@ -1,113 +0,0 @@
-#!/usr/bin/python
-import optparse
-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():
-  parser = optparse.OptionParser()
-  parser.add_option('-e', '--eland', dest='inname',
-                    help='specify input eland filename')
-  parser.add_option('-b', '--bed', dest='outname',
-                    help='specify output befilename')
-  parser.add_option('-n', '--name', dest='name',
-                    help='specify the track (short) name.',
-                    default=None)
-  parser.add_option('-d', '--description', dest='description',
-                    help='specify the track description',
-                    default=None)
-  parser.add_option('--chromosome', dest='prefix',
-                    help='Set the chromosome prefix name. defaults to "chr"',
-                    default='chr')
-  parser.add_option("--database", dest='database',
-                    help="specify location of fctracker database",
-                    default=None)
-  parser.add_option("--flowcell", dest='flowcell',
-                    help="compute name and description from database using flowcell id",
-                    default=None)
-  parser.add_option("--lane", dest='lane',
-                    help='specify which lane to use when retrieving description from database',
-                    default=None)
-
-  multi = optparse.OptionGroup(parser, 'Multi-read ELAND support')
-
-  multi.add_option('-m', '--multi', action='store_true',
-                    help='Enable parsing multi-read eland files',
-                    default=False)
-  multi.add_option('--reads', type='int',
-                   help='limit reporting multi reads to this many reads'
-                        '(most usefully --reads=1 will turn a multi-read '
-                        'file into a single read file)',
-                   default=255)
-  parser.add_option_group(multi)
-
-  return parser
-
-def main(command_line=None):
-  instream = None
-  outstream = None
-
-  if command_line is None:
-    command_line = sys.argv[1:]
-
-  parser = make_parser()
-  (options, args) = parser.parse_args(command_line)
-
-  if options.inname is None:
-    parser.error("Need eland input file name")
-    return 1
-
-  if options.inname == '-':
-    instream = sys.stdin
-  elif os.path.exists(options.inname):
-    instream = autoopen(options.inname, 'r')
-  else:
-    parser.error('%s was not found' % (options.inname))
-    return 1
-
-  # figure out name for output file
-  if options.outname is None:
-      # if outname wasn't defined, and we're reading from stdout
-      if instream is sys.stdin:
-          # write to stdout
-          outstream = sys.stdout
-      else:
-          # if there's a name write to name.bed
-          options.outname = os.path.splitext(options.inname)[0]+'.bed'
-          print >>sys.stderr, "defaulting to outputname", options.outname
-  elif options.outname == '-':
-      outstream = sys.stdout
-
-  if outstream is None:
-      if os.path.exists(options.outname):
-          parser.error("not overwriting %s" % (options.outname))
-          return 1
-      else:
-          outstream = open(options.outname, 'w')
-
-  if options.flowcell is not None and options.lane is not None:
-    # get our name/description out of the database
-    name, description = make_description(
-                           options.database, options.flowcell, options.lane
-                        )
-  else:
-    name = options.name
-    description = options.description
-
-  if options.multi:
-    make_bed_from_multi_eland_stream(instream, outstream, 
-                                     name, description, 
-                                     options.prefix,
-                                     options.reads)
-
-  else:
-    make_bed_from_eland_stream(instream, outstream, 
-                               name, description, 
-                               options.prefix)
-  return 0
-
-if __name__ == "__main__":
-  sys.exit(main(sys.argv[1:]))
-