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

[htsworkflow.git] / scripts / htsw-eland2bed

diff --git a/scripts/htsw-eland2bed b/scripts/htsw-eland2bed
new file mode 100755 (executable)
index 0000000..577b868
--- /dev/null
+++ b/scripts/htsw-eland2bed
@@ -0,0 +1,113 @@
+#!/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:]))
+