Rename all the scripts to start with htsw-

[htsworkflow.git] / scripts / gerald2bed.py

diff --git a/scripts/gerald2bed.py b/scripts/gerald2bed.py
deleted file mode 100644 (file)
index 7a726e7..0000000
--- a/scripts/gerald2bed.py
+++ /dev/null
@@ -1,96 +0,0 @@
-#!/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 htsworkflow.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:]))
-