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 LOGGER = logging.getLogger(__name__)
  14
  15 def make_bed_for_gerald(eland_dir, output_dir, prefix, database, flowcell):
  16     """
  17     convert s_[1-8]_eland_result.txt to corresponding bed files
  18     """
  19     eland_files = glob(os.path.join(eland_dir, 's_[1-8]_eland_result.txt'))
  20     out_files = glob(os.path.join(eland_dir, 's_[1-8]_eland_result.bed'))
  21     if len(out_files) > 0:
  22         raise RuntimeError("please move old bedfiles")
  23
  24     LOGGER.info('Processing %s using flowcell id %s' % (eland_dir, flowcell))
  25     for pathname in eland_files:
  26         path, name = os.path.split(pathname)
  27         lane = int(name[2])
  28         outname = 's_%d_eland_result.bed' %(lane,)
  29         LOGGER.info('Converting lane %d to %s' % (lane, outname))
  30
  31         outpathname = os.path.join(eland_dir, outname)
  32         # look up descriptions
  33         bed_name, description = make_description(database, flowcell, lane)
  34
  35         # open files
  36         instream = open(pathname,'r')
  37         outstream = open(outpathname,'w')
  38
  39         make_bed_from_eland_stream(
  40           instream, outstream, name, description, prefix
  41         )
  42
  43 def make_parser():
  44   usage = """%prog: --flowcell <flowcell id> directory_name
  45
  46 directory should contain a set of 8 eland result files named like
  47 s_[12345678]_eland_result.txt"""
  48
  49
  50   parser = optparse.OptionParser(usage)
  51
  52   parser.add_option('-o', '--output', dest='output',
  53                     help="destination directory for our bed files" \
  54                          "defaults to eland directory",
  55                     default=None)
  56   parser.add_option('--chromosome', dest='prefix',
  57                     help='Set the chromosome prefix name. defaults to "chr"',
  58                     default='chr')
  59   parser.add_option("--database", dest='database',
  60                     help="specify location of fctracker database",
  61                     default=None)
  62   parser.add_option("--flowcell", dest='flowcell',
  63                     help="specify the flowcell id for this run",
  64                     default=None)
  65   parser.add_option('-v', '--verbose', dest='verbose', action='store_true',
  66                     help='increase verbosity',
  67                     default=False)
  68   return parser
  69
  70 def main(command_line=None):
  71     LOGGER.basicConfig(level=logging.WARNING)
  72     if command_line is None:
  73         command_line = sys.argv[1:]
  74
  75     parser = make_parser()
  76     (opts, args) = parser.parse_args(command_line)
  77
  78     if len(args) != 1:
  79         parser.error('Directory name required')
  80
  81     eland_dir = args[0]
  82     if not os.path.isdir(eland_dir):
  83         parser.error('%s must be a directory' % (eland_dir,))
  84
  85     if opts.flowcell is None:
  86         parser.error('Flowcell ID required')
  87
  88     if opts.verbose:
  89         logger = logging.getLogger()
  90         logger.setLevel(logging.INFO)
  91
  92     make_bed_for_gerald(eland_dir, opts.output, opts.prefix, opts.database, opts.flowcell)
  93
  94     return 0
  95
  96 if __name__ == "__main__":
  97     sys.exit(main(sys.argv[1:]))
  98