Add a script that takes a set of eland_result files and makes bedfiles

it'll also look up the lane descriptions in the flowcell database

diff --git a/scripts/gerald2bed.py b/scripts/gerald2bed.py
new file mode 100644 (file)
index 0000000..c49cc9c
--- /dev/null
+++ b/scripts/gerald2bed.py
@@ -0,0 +1,96 @@
+#!/usr/bin/python
+"""
+Convert a group of eland_result files from a sequencer run to bed files.
+"""
+from glob import glob
+import logging
+import optparse
+import sys
+import os
+
+from gaworkflow.util.makebed import make_bed_from_eland_stream, make_description
+
+def make_bed_for_gerald(eland_dir, output_dir, prefix, database, flowcell):
+    """
+    convert s_[1-8]_eland_result.txt to corresponding bed files
+    """
+    eland_files = glob(os.path.join(eland_dir, 's_[1-8]_eland_result.txt'))
+    out_files = glob(os.path.join(eland_dir, 's_[1-8]_eland_result.bed'))
+    if len(out_files) > 0:
+        raise RuntimeError("please move old bedfiles")
+
+    logging.info('Processing %s using flowcell id %s' % (eland_dir, flowcell))
+    for pathname in eland_files:
+        path, name = os.path.split(pathname)
+        lane = int(name[2])
+        outname = 's_%d_eland_result.bed' %(lane,)
+        logging.info('Converting lane %d to %s' % (lane, outname))
+
+        outpathname = os.path.join(eland_dir, outname)
+        # look up descriptions
+        bed_name, description = make_description(database, flowcell, lane)
+
+        # open files
+        instream = open(pathname,'r')
+        outstream = open(outpathname,'w')
+
+        make_bed_from_eland_stream(
+          instream, outstream, name, description, prefix
+        )
+
+def make_parser():
+  usage = """%prog: --flowcell <flowcell id> directory_name
+
+directory should contain a set of 8 eland result files named like
+s_[12345678]_eland_result.txt"""
+
+
+  parser = optparse.OptionParser(usage)
+
+  parser.add_option('-o', '--output', dest='output',
+                    help="destination directory for our bed files" \
+                         "defaults to eland directory",
+                    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="specify the flowcell id for this run",
+                    default=None)
+  parser.add_option('-v', '--verbose', dest='verbose', action='store_true',
+                    help='increase verbosity',
+                    default=False)
+  return parser
+
+def main(command_line=None):
+    logging.basicConfig(level=logging.WARNING)
+    if command_line is None:
+        command_line = sys.argv[1:]
+
+    parser = make_parser()
+    (opts, args) = parser.parse_args(command_line)
+
+    if len(args) != 1:
+        parser.error('Directory name required')
+
+    eland_dir = args[0]
+    if not os.path.isdir(eland_dir):
+        parser.error('%s must be a directory' % (eland_dir,))
+
+    if opts.flowcell is None:
+        parser.error('Flowcell ID required')
+
+    if opts.verbose:
+        logger = logging.getLogger()
+        logger.setLevel(logging.INFO)
+
+    make_bed_for_gerald(eland_dir, opts.output, opts.prefix, opts.database, opts.flowcell)
+
+    return 0
+
+if __name__ == "__main__":
+    sys.exit(main(sys.argv[1:]))
+