scripts/htsw-gerald2bed

   1 #!/usr/bin/python
   2 """
   3 Convert a group of eland_result files from a sequencer run to bed files.
   4 """
   5 from glob import glob
   6 import logging
   7 import optparse
   8 import sys
   9 import os
  10
  11 from htsworkflow.util.makebed import make_bed_from_eland_stream, make_description
  12
  13 def make_bed_for_gerald(eland_dir, output_dir, prefix, database, flowcell):
  14     """
  15     convert s_[1-8]_eland_result.txt to corresponding bed files
  16     """
  17     eland_files = glob(os.path.join(eland_dir, 's_[1-8]_eland_result.txt'))
  18     out_files = glob(os.path.join(eland_dir, 's_[1-8]_eland_result.bed'))
  19     if len(out_files) > 0:
  20         raise RuntimeError("please move old bedfiles")
  21
  22     logging.info('Processing %s using flowcell id %s' % (eland_dir, flowcell))
  23     for pathname in eland_files:
  24         path, name = os.path.split(pathname)
  25         lane = int(name[2])
  26         outname = 's_%d_eland_result.bed' %(lane,)
  27         logging.info('Converting lane %d to %s' % (lane, outname))
  28
  29         outpathname = os.path.join(eland_dir, outname)
  30         # look up descriptions
  31         bed_name, description = make_description(database, flowcell, lane)
  32
  33         # open files
  34         instream = open(pathname,'r')
  35         outstream = open(outpathname,'w')
  36
  37         make_bed_from_eland_stream(
  38           instream, outstream, name, description, prefix
  39         )
  40
  41 def make_parser():
  42   usage = """%prog: --flowcell <flowcell id> directory_name
  43
  44 directory should contain a set of 8 eland result files named like
  45 s_[12345678]_eland_result.txt"""
  46
  47
  48   parser = optparse.OptionParser(usage)
  49
  50   parser.add_option('-o', '--output', dest='output',
  51                     help="destination directory for our bed files" \
  52                          "defaults to eland directory",
  53                     default=None)
  54   parser.add_option('--chromosome', dest='prefix',
  55                     help='Set the chromosome prefix name. defaults to "chr"',
  56                     default='chr')
  57   parser.add_option("--database", dest='database',
  58                     help="specify location of fctracker database",
  59                     default=None)
  60   parser.add_option("--flowcell", dest='flowcell',
  61                     help="specify the flowcell id for this run",
  62                     default=None)
  63   parser.add_option('-v', '--verbose', dest='verbose', action='store_true',
  64                     help='increase verbosity',
  65                     default=False)
  66   return parser
  67
  68 def main(command_line=None):
  69     logging.basicConfig(level=logging.WARNING)
  70     if command_line is None:
  71         command_line = sys.argv[1:]
  72
  73     parser = make_parser()
  74     (opts, args) = parser.parse_args(command_line)
  75
  76     if len(args) != 1:
  77         parser.error('Directory name required')
  78
  79     eland_dir = args[0]
  80     if not os.path.isdir(eland_dir):
  81         parser.error('%s must be a directory' % (eland_dir,))
  82
  83     if opts.flowcell is None:
  84         parser.error('Flowcell ID required')
  85
  86     if opts.verbose:
  87         logger = logging.getLogger()
  88         logger.setLevel(logging.INFO)
  89
  90     make_bed_for_gerald(eland_dir, opts.output, opts.prefix, opts.database, opts.flowcell)
  91
  92     return 0
  93
  94 if __name__ == "__main__":
  95     sys.exit(main(sys.argv[1:]))
  96