Mercurial > repos > nick > dna_visualizer
comparison literal.py @ 5:58160195728e
Change color setting UI, allow background color setting, limit image size.
author | Nick Stoler <nstoler@psu.edu> |
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date | Sun, 02 Mar 2014 22:01:44 -0500 |
parents | 5257ce9d9184 |
children |
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4:16772d7246e0 | 5:58160195728e |
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4 import sys | 4 import sys |
5 import Image | 5 import Image |
6 import argparse | 6 import argparse |
7 import fastareader | 7 import fastareader |
8 | 8 |
9 OPT_DEFAULTS = {'size':'512x512', 'verbose':True, | 9 OPT_DEFAULTS = {'size':'512x512', 'verbose':True, 'background':'255,255,255', |
10 'A':'0,255,0', 'T':'255,0,0', 'G':'255,255,255', 'C':'0,0,255'} | 10 'A':'0,255,0', 'T':'255,0,0', 'G':'255,255,255', 'C':'0,0,255'} |
11 USAGE = "%(prog)s [options] genome.fasta" | 11 USAGE = "%(prog)s [options] genome.fasta" |
12 DESCRIPTION = """Convert DNA sequence into a PNG image by representing each base | 12 DESCRIPTION = """Convert DNA sequence into a PNG image by representing each base |
13 with one colored pixel.""" | 13 with one colored pixel.""" |
14 EPILOG = """""" | 14 EPILOG = """""" |
38 parser.add_argument('-v', '--verbose', action='store_true', | 38 parser.add_argument('-v', '--verbose', action='store_true', |
39 help="""Verbose mode. On by default.""") | 39 help="""Verbose mode. On by default.""") |
40 parser.add_argument('-q', '--quiet', action='store_false', dest='verbose', | 40 parser.add_argument('-q', '--quiet', action='store_false', dest='verbose', |
41 help="""Quiet mode.""") | 41 help="""Quiet mode.""") |
42 group = parser.add_argument_group('Color customization', """Use these options | 42 group = parser.add_argument_group('Color customization', """Use these options |
43 to use custom colors for bases. Specify with a comma-delimited RGB value | 43 to use custom colors for the background and the bases. Specify with a |
44 like "100,150,10".""") | 44 comma-delimited RGB value like "100,150,10".""") |
45 group.add_argument('-b', '--background', metavar='R,G,B', | |
46 help="""default: %(default)s""") | |
45 group.add_argument('-A', metavar='R,G,B', | 47 group.add_argument('-A', metavar='R,G,B', |
46 help="""default: %(default)s""") | 48 help="""default: %(default)s""") |
47 group.add_argument('-T', metavar='R,G,B', | 49 group.add_argument('-T', metavar='R,G,B', |
48 help="""default: %(default)s""") | 50 help="""default: %(default)s""") |
49 group.add_argument('-G', metavar='R,G,B', | 51 group.add_argument('-G', metavar='R,G,B', |
52 help="""default: %(default)s""") | 54 help="""default: %(default)s""") |
53 | 55 |
54 args = parser.parse_args() | 56 args = parser.parse_args() |
55 | 57 |
56 try: | 58 try: |
57 size = parse_size(args.size) | 59 size = parse_int_str(args.size, delim='x', num_ints=2) |
58 except ValueError: | 60 except ValueError: |
59 parser.print_help() | 61 parser.print_help() |
60 fail('\nError: Invalid size string "%s".' % args.size) | 62 fail('\nError: Invalid size string "%s".' % args.size) |
61 | 63 |
62 fasta = fastareader.FastaLineGenerator(args.fasta) | 64 fasta = fastareader.FastaLineGenerator(args.fasta) |
65 if not args.display: | 67 if not args.display: |
66 outfile = args.outfile if args.outfile else outfile_name(args.fasta) | 68 outfile = args.outfile if args.outfile else outfile_name(args.fasta) |
67 if os.path.exists(outfile) and not args.clobber: | 69 if os.path.exists(outfile) and not args.clobber: |
68 fail('Error: Output filename already taken: "%s"' % outfile) | 70 fail('Error: Output filename already taken: "%s"' % outfile) |
69 | 71 |
72 background = parse_int_str(args.background) | |
73 | |
70 colors = {} | 74 colors = {} |
71 colors['A'] = parse_rgb(args.A) | 75 colors['A'] = parse_int_str(args.A) |
72 colors['T'] = parse_rgb(args.T) | 76 colors['T'] = parse_int_str(args.T) |
73 colors['G'] = parse_rgb(args.G) | 77 colors['G'] = parse_int_str(args.G) |
74 colors['C'] = parse_rgb(args.C) | 78 colors['C'] = parse_int_str(args.C) |
75 | 79 |
76 image = Image.new('RGB', size, 'white') | 80 image = Image.new('RGB', size, background) |
77 pixels = image.load() | 81 pixels = image.load() |
78 | 82 |
79 done = False | 83 done = False |
80 for i in range(image.size[1]): | 84 for i in range(image.size[1]): |
81 for j in range(image.size[0]): | 85 for j in range(image.size[0]): |
93 image.show() | 97 image.show() |
94 else: | 98 else: |
95 image.save(outfile, 'PNG') | 99 image.save(outfile, 'PNG') |
96 | 100 |
97 | 101 |
98 | 102 def parse_int_str(string, delim=',', num_ints=3): |
99 def parse_size(size_str): | 103 """Parse string of delimited ints, return them in a tuple. |
100 """Parse size string, return a tuple of (width, height). | 104 Checks that they are ints, they are delimited by "delim", and there are |
101 Accepts size strings in the format "640x480". | 105 "num_ints" of them. |
102 If not valid, raises ValueError.""" | 106 If not valid, raises ValueError.""" |
103 size = map(int, size_str.split('x')) | 107 ints = map(int, string.split(delim)) |
104 if len(size) != 2: | 108 if len(ints) != num_ints: |
105 raise ValueError | 109 raise ValueError |
106 else: | 110 else: |
107 return tuple(size) | 111 return tuple(ints) |
108 | |
109 | |
110 def parse_rgb(rgb_str): | |
111 """Parse RGB string, return a tuple of (R, G, B). | |
112 If not valid, raises ValueError.""" | |
113 rgb = map(int, rgb_str.split(',')) | |
114 if len(rgb) != 3: | |
115 raise ValueError | |
116 else: | |
117 return tuple(rgb) | |
118 | 112 |
119 | 113 |
120 def outfile_name(infilename): | 114 def outfile_name(infilename): |
121 base = infilename.split('.')[0] | 115 base = infilename.split('.')[0] |
122 if not base: | 116 if not base: |