comparison literal.py @ 5:58160195728e

Change color setting UI, allow background color setting, limit image size.

4:16772d7246e0

import sys
import Image
import argparse
import fastareader

OPT_DEFAULTS = {'size':'512x512', 'verbose':True,
  'A':'0,255,0', 'T':'255,0,0', 'G':'255,255,255', 'C':'0,0,255'}
USAGE = "%(prog)s [options] genome.fasta"
DESCRIPTION = """Convert DNA sequence into a PNG image by representing each base
  with one colored pixel."""
EPILOG = """"""

  parser.add_argument('-v', '--verbose', action='store_true',
    help="""Verbose mode. On by default.""")
  parser.add_argument('-q', '--quiet', action='store_false', dest='verbose',
    help="""Quiet mode.""")
  group = parser.add_argument_group('Color customization', """Use these options
    to use custom colors for bases. Specify with a comma-delimited RGB value
    like "100,150,10".""")
  group.add_argument('-A', metavar='R,G,B',
    help="""default: %(default)s""")
  group.add_argument('-T', metavar='R,G,B',
    help="""default: %(default)s""")
  group.add_argument('-G', metavar='R,G,B',

    help="""default: %(default)s""")

  args = parser.parse_args()

  try:
    size = parse_size(args.size)
  except ValueError:
    parser.print_help()
    fail('\nError: Invalid size string "%s".' % args.size)

  fasta = fastareader.FastaLineGenerator(args.fasta)

  if not args.display:
    outfile = args.outfile if args.outfile else outfile_name(args.fasta)
    if os.path.exists(outfile) and not args.clobber:
      fail('Error: Output filename already taken: "%s"' % outfile)

  colors = {}
  colors['A'] = parse_rgb(args.A)
  colors['T'] = parse_rgb(args.T)
  colors['G'] = parse_rgb(args.G)
  colors['C'] = parse_rgb(args.C)

  image = Image.new('RGB', size, 'white')
  pixels = image.load()

  done = False
  for i in range(image.size[1]):
    for j in range(image.size[0]):

    image.show()
  else:
    image.save(outfile, 'PNG')



def parse_size(size_str):
  """Parse size string, return a tuple of (width, height).
  Accepts size strings in the format "640x480".
  If not valid, raises ValueError."""
  size = map(int, size_str.split('x'))
  if len(size) != 2:
    raise ValueError
  else:
    return tuple(size)


def parse_rgb(rgb_str):
  """Parse RGB string, return a tuple of (R, G, B).
  If not valid, raises ValueError."""
  rgb = map(int, rgb_str.split(','))
  if len(rgb) != 3:
    raise ValueError
  else:
    return tuple(rgb)


def outfile_name(infilename):
  base = infilename.split('.')[0]
  if not base:

5:58160195728e

import sys
import Image
import argparse
import fastareader

OPT_DEFAULTS = {'size':'512x512', 'verbose':True, 'background':'255,255,255',
  'A':'0,255,0', 'T':'255,0,0', 'G':'255,255,255', 'C':'0,0,255'}
USAGE = "%(prog)s [options] genome.fasta"
DESCRIPTION = """Convert DNA sequence into a PNG image by representing each base
  with one colored pixel."""
EPILOG = """"""

  parser.add_argument('-v', '--verbose', action='store_true',
    help="""Verbose mode. On by default.""")
  parser.add_argument('-q', '--quiet', action='store_false', dest='verbose',
    help="""Quiet mode.""")
  group = parser.add_argument_group('Color customization', """Use these options
    to use custom colors for the background and the bases. Specify with a
    comma-delimited RGB value like "100,150,10".""")
  group.add_argument('-b', '--background', metavar='R,G,B',
    help="""default: %(default)s""")
  group.add_argument('-A', metavar='R,G,B',
    help="""default: %(default)s""")
  group.add_argument('-T', metavar='R,G,B',
    help="""default: %(default)s""")
  group.add_argument('-G', metavar='R,G,B',

    help="""default: %(default)s""")

  args = parser.parse_args()

  try:
    size = parse_int_str(args.size, delim='x', num_ints=2)
  except ValueError:
    parser.print_help()
    fail('\nError: Invalid size string "%s".' % args.size)

  fasta = fastareader.FastaLineGenerator(args.fasta)

  if not args.display:
    outfile = args.outfile if args.outfile else outfile_name(args.fasta)
    if os.path.exists(outfile) and not args.clobber:
      fail('Error: Output filename already taken: "%s"' % outfile)

  background = parse_int_str(args.background)

  colors = {}
  colors['A'] = parse_int_str(args.A)
  colors['T'] = parse_int_str(args.T)
  colors['G'] = parse_int_str(args.G)
  colors['C'] = parse_int_str(args.C)

  image = Image.new('RGB', size, background)
  pixels = image.load()

  done = False
  for i in range(image.size[1]):
    for j in range(image.size[0]):

    image.show()
  else:
    image.save(outfile, 'PNG')


def parse_int_str(string, delim=',', num_ints=3):
  """Parse string of delimited ints, return them in a tuple.
  Checks that they are ints, they are delimited by "delim", and there are
  "num_ints" of them.
  If not valid, raises ValueError."""
  ints = map(int, string.split(delim))
  if len(ints) != num_ints:
    raise ValueError
  else:
    return tuple(ints)


def outfile_name(infilename):
  base = infilename.split('.')[0]
  if not base: