text: #!/usr/bin/env python
  
  """
  Read a table dump in the UCSC gene table format and print a tab separated
  list of intervals corresponding to requested features of each gene.
  
  usage: ucsc_gene_table_to_intervals.py [options]
  
  options:
    -h, --help                  show this help message and exit
    -rREGION, --region=REGION
                                Limit to region: one of coding, utr3, utr5, transcribed [default]
    -e, --exons                 Only print intervals overlapping an exon
    -i, --input=inputfile       input file
    -o, --output=outputfile     output file
  """
  
  import optparse
  import string
  import sys
  
  assert sys.version_info[:2] >= ( 2, 4 )
  
  
  def main():
      parser = optparse.OptionParser( usage="%prog [options] " )
      parser.add_option( "-r", "--region", dest="region", default="transcribed",
                         help="Limit to region: one of coding, utr3, utr5, transcribed [default]" )
      parser.add_option( "-e", "--exons", action="store_true", dest="exons",
                         help="Only print intervals overlapping an exon" )
      parser.add_option( "-s", "--strand", action="store_true", dest="strand",
                         help="Print strand after interval" )
      parser.add_option( "-i", "--input", dest="input", default=None,
                         help="Input file" )
      parser.add_option( "-o", "--output", dest="output", default=None,
                         help="Output file" )
      options, args = parser.parse_args()
      assert options.region in ( 'coding', 'utr3', 'utr5', 'transcribed' ), "Invalid region argument"
  
      try:
          out_file = open(options.output, "w")
      except:
          print >> sys.stderr, "Bad output file."
          sys.exit(0)
  
      try:
          in_file = open(options.input)
      except:
          print >> sys.stderr, "Bad input file."
          sys.exit(0)
  
      print "Region:", options.region + ";"
      print "Only overlap with Exons:",
      if options.exons:
          print "Yes"
      else:
          print "No"
  
      # Read table and handle each gene
      for line in in_file:
          try:
              if line[0:1] == "#":
                  continue
              # Parse fields from gene tabls
              fields = line.split( '\t' )
              name = fields[0]
              chrom = fields[1]
              strand = fields[2].replace(" ", "_")
              tx_start = int( fields[3] )
              tx_end = int( fields[4] )
              cds_start = int( fields[5] )
              cds_end = int( fields[6] )
  
              # Determine the subset of the transcribed region we are interested in
              if options.region == 'utr3':
                  if strand == '-':
                      region_start, region_end = tx_start, cds_start
                  else:
                      region_start, region_end = cds_end, tx_end
              elif options.region == 'utr5':
                  if strand == '-':
                      region_start, region_end = cds_end, tx_end
                  else:
                      region_start, region_end = tx_start, cds_start
              elif options.region == 'coding':
                  region_start, region_end = cds_start, cds_end
              else:
                  region_start, region_end = tx_start, tx_end
  
              # If only interested in exons, print the portion of each exon overlapping
              # the region of interest, otherwise print the span of the region
              if options.exons:
                  exon_starts = map( int, fields[8].rstrip( ',\n' ).split( ',' ) )
                  exon_ends = map( int, fields[9].rstrip( ',\n' ).split( ',' ) )
                  for start, end in zip( exon_starts, exon_ends ):
                      start = max( start, region_start )
                      end = min( end, region_end )
                      if start < end:
                          if strand:
                              print_tab_sep(out_file, chrom, start, end, name, "0", strand )
                          else:
                              print_tab_sep(out_file, chrom, start, end )
              else:
                  if strand:
                      print_tab_sep(out_file, chrom, region_start, region_end, name, "0", strand )
                  else:
                      print_tab_sep(out_file, chrom, region_start, region_end )
          except:
              continue
  
  
  def print_tab_sep(out_file, *args ):
      """Print items in `l` to stdout separated by tabs"""
      print >>out_file, string.join( [ str( f ) for f in args ], '\t' )
  
  if __name__ == "__main__":
      main()
  