Mercurial > repos > nick > dna_visualizer
annotate literal.py @ 10:54223991334b default tip
tool_dependencies.xml: Defined PIL dependency
| author | Nick Stoler <nstoler@psu.edu> |
|---|---|
| date | Mon, 03 Mar 2014 12:54:02 -0500 |
| parents | 58160195728e |
| children |
| rev | line source |
|---|---|
| 0 | 1 #!/usr/bin/env python |
| 2 from __future__ import division | |
| 3 import os | |
| 4 import sys | |
| 5 import Image | |
| 6 import argparse | |
| 7 import fastareader | |
| 8 | |
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9 OPT_DEFAULTS = {'size':'512x512', 'verbose':True, 'background':'255,255,255', |
| 0 | 10 'A':'0,255,0', 'T':'255,0,0', 'G':'255,255,255', 'C':'0,0,255'} |
| 11 USAGE = "%(prog)s [options] genome.fasta" | |
| 12 DESCRIPTION = """Convert DNA sequence into a PNG image by representing each base | |
| 13 with one colored pixel.""" | |
| 14 EPILOG = """""" | |
| 15 | |
| 16 def main(): | |
| 17 | |
| 18 parser = argparse.ArgumentParser( | |
| 19 description=DESCRIPTION, usage=USAGE, epilog=EPILOG) | |
| 20 parser.set_defaults(**OPT_DEFAULTS) | |
| 21 | |
| 22 parser.add_argument('fasta', metavar='genome.fasta', | |
| 23 help="""Input sequence. Can be in FASTA format or a plain text file | |
| 24 containing only the sequence. Any non-ATGC characters (case-insensitive) | |
| 25 will be skipped.""") | |
| 26 parser.add_argument('-s', '--size', | |
| 27 help="""The output image size, in pixels, in the format "widthxheight", e.g. | |
| 28 "640x480". If the sequence is larger than the number of pixels in the | |
| 29 image, it will be cut off. Default size: %(default)s""") | |
| 30 parser.add_argument('-o', '--outfile', metavar='image.png', | |
| 31 help="""Output filename. Overrides the default, which is | |
| 32 to use the input filename base plus .png.""") | |
| 33 parser.add_argument('-d', '--display', action='store_true', | |
| 34 help="""Display the image instead of saving it.""") | |
| 35 parser.add_argument('-c', '--clobber', action='store_true', | |
| 36 help="""If the output filename already exists, overwrite it instead of | |
| 37 throwing an error (the default).""") | |
| 38 parser.add_argument('-v', '--verbose', action='store_true', | |
| 39 help="""Verbose mode. On by default.""") | |
| 40 parser.add_argument('-q', '--quiet', action='store_false', dest='verbose', | |
| 41 help="""Quiet mode.""") | |
| 42 group = parser.add_argument_group('Color customization', """Use these options | |
|
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58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
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diff
changeset
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43 to use custom colors for the background and the bases. Specify with a |
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58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
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diff
changeset
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44 comma-delimited RGB value like "100,150,10".""") |
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58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
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diff
changeset
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45 group.add_argument('-b', '--background', metavar='R,G,B', |
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58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
0
diff
changeset
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46 help="""default: %(default)s""") |
| 0 | 47 group.add_argument('-A', metavar='R,G,B', |
| 48 help="""default: %(default)s""") | |
| 49 group.add_argument('-T', metavar='R,G,B', | |
| 50 help="""default: %(default)s""") | |
| 51 group.add_argument('-G', metavar='R,G,B', | |
| 52 help="""default: %(default)s""") | |
| 53 group.add_argument('-C', metavar='R,G,B', | |
| 54 help="""default: %(default)s""") | |
| 55 | |
| 56 args = parser.parse_args() | |
| 57 | |
| 58 try: | |
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59 size = parse_int_str(args.size, delim='x', num_ints=2) |
| 0 | 60 except ValueError: |
| 61 parser.print_help() | |
| 62 fail('\nError: Invalid size string "%s".' % args.size) | |
| 63 | |
| 64 fasta = fastareader.FastaLineGenerator(args.fasta) | |
| 65 bases = fasta.bases() | |
| 66 | |
| 67 if not args.display: | |
| 68 outfile = args.outfile if args.outfile else outfile_name(args.fasta) | |
| 69 if os.path.exists(outfile) and not args.clobber: | |
| 70 fail('Error: Output filename already taken: "%s"' % outfile) | |
| 71 | |
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parents:
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72 background = parse_int_str(args.background) |
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parents:
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73 |
| 0 | 74 colors = {} |
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75 colors['A'] = parse_int_str(args.A) |
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58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
0
diff
changeset
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76 colors['T'] = parse_int_str(args.T) |
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58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
0
diff
changeset
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77 colors['G'] = parse_int_str(args.G) |
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58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
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diff
changeset
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78 colors['C'] = parse_int_str(args.C) |
| 0 | 79 |
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58160195728e
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parents:
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diff
changeset
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80 image = Image.new('RGB', size, background) |
| 0 | 81 pixels = image.load() |
| 82 | |
| 83 done = False | |
| 84 for i in range(image.size[1]): | |
| 85 for j in range(image.size[0]): | |
| 86 try: | |
| 87 base = next(bases).upper() | |
| 88 except StopIteration: | |
| 89 done = True | |
| 90 break | |
| 91 if base in colors: | |
| 92 pixels[j,i] = colors[base] | |
| 93 if done: | |
| 94 break | |
| 95 | |
| 96 if args.display: | |
| 97 image.show() | |
| 98 else: | |
| 99 image.save(outfile, 'PNG') | |
| 100 | |
| 101 | |
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58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
0
diff
changeset
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102 def parse_int_str(string, delim=',', num_ints=3): |
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58160195728e
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parents:
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diff
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103 """Parse string of delimited ints, return them in a tuple. |
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58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
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diff
changeset
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104 Checks that they are ints, they are delimited by "delim", and there are |
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58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
0
diff
changeset
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105 "num_ints" of them. |
| 0 | 106 If not valid, raises ValueError.""" |
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58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
0
diff
changeset
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107 ints = map(int, string.split(delim)) |
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58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
0
diff
changeset
|
108 if len(ints) != num_ints: |
| 0 | 109 raise ValueError |
| 110 else: | |
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58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
0
diff
changeset
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111 return tuple(ints) |
| 0 | 112 |
| 113 | |
| 114 def outfile_name(infilename): | |
| 115 base = infilename.split('.')[0] | |
| 116 if not base: | |
| 117 base = infilename | |
| 118 return base+'.png' | |
| 119 | |
| 120 | |
| 121 def fail(message): | |
| 122 sys.stderr.write(message+"\n") | |
| 123 sys.exit(1) | |
| 124 | |
| 125 if __name__ == '__main__': | |
| 126 main() |