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comparison bin/last-dotplot @ 0:06f8460885ff

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author yutaka-saito
date Sun, 19 Apr 2015 20:51:13 +0900
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-1:000000000000 0:06f8460885ff
1 #! /usr/bin/env python
2
3 # Read pair-wise alignments in MAF or LAST tabular format: write an
4 # "Oxford grid", a.k.a. dotplot.
5
6 # TODO: Currently, pixels with zero aligned nt-pairs are white, and
7 # pixels with one or more aligned nt-pairs are black. This can look
8 # too crowded for large genome alignments. I tried shading each pixel
9 # according to the number of aligned nt-pairs within it, but the
10 # result is too faint. How can this be done better?
11
12 import fileinput, itertools, optparse, os, re, sys
13
14 # Try to make PIL/PILLOW work:
15 try: from PIL import Image, ImageDraw, ImageFont, ImageColor
16 except ImportError: import Image, ImageDraw, ImageFont, ImageColor
17
18 my_name = os.path.basename(sys.argv[0])
19 usage = """
20 %prog --help
21 %prog [options] last-tabular-output dotplot.png
22 %prog [options] last-tabular-output dotplot.gif
23 etc."""
24 parser = optparse.OptionParser(usage=usage)
25 # Replace "width" & "height" with a single "length" option?
26 parser.add_option("-x", "--width", type="int", dest="width", default=1000,
27 help="maximum width in pixels (default: %default)")
28 parser.add_option("-y", "--height", type="int", dest="height", default=1000,
29 help="maximum height in pixels (default: %default)")
30 parser.add_option("-f", "--fontfile", dest="fontfile",
31 help="TrueType or OpenType font file")
32 parser.add_option("-s", "--fontsize", type="int", dest="fontsize", default=11,
33 help="TrueType or OpenType font size (default: %default)")
34 parser.add_option("-c", "--forwardcolor", dest="forwardcolor", default="red",
35 help="Color for forward alignments (default: %default)")
36 parser.add_option("-r", "--reversecolor", dest="reversecolor", default="blue",
37 help="Color for reverse alignments (default: %default)")
38 (opts, args) = parser.parse_args()
39 if len(args) != 2: parser.error("2 arguments needed")
40
41 if opts.fontfile: font = ImageFont.truetype(opts.fontfile, opts.fontsize)
42 else: font = ImageFont.load_default()
43
44 # Make these options too?
45 text_color = "black"
46 background_color = "white"
47 pix_tween_seqs = 2 # number of border pixels between sequences
48 border_shade = 239, 239, 239 # the shade of grey to use for border pixels
49 label_space = 5 # minimum number of pixels between axis labels
50
51 image_mode = 'RGB'
52 forward_color = ImageColor.getcolor(opts.forwardcolor, image_mode)
53 reverse_color = ImageColor.getcolor(opts.reversecolor, image_mode)
54 overlap_color = tuple([(i+j)//2 for i, j in zip(forward_color, reverse_color)])
55
56 def tabBlocks(beg1, beg2, blocks):
57 '''Get the gapless blocks of an alignment, from LAST tabular format.'''
58 for i in blocks.split(","):
59 if ":" in i:
60 x, y = i.split(":")
61 beg1 += int(x)
62 beg2 += int(y)
63 else:
64 size = int(i)
65 yield beg1, beg2, size
66 beg1 += size
67 beg2 += size
68
69 def mafBlocks(beg1, beg2, seq1, seq2):
70 '''Get the gapless blocks of an alignment, from MAF format.'''
71 size = 0
72 for x, y in itertools.izip(seq1, seq2):
73 if x == "-":
74 if size:
75 yield beg1, beg2, size
76 beg1 += size
77 beg2 += size
78 size = 0
79 beg2 += 1
80 elif y == "-":
81 if size:
82 yield beg1, beg2, size
83 beg1 += size
84 beg2 += size
85 size = 0
86 beg1 += 1
87 else:
88 size += 1
89 if size: yield beg1, beg2, size
90
91 def alignmentInput(lines):
92 '''Get alignments and sequence lengths, from MAF or tabular format.'''
93 mafCount = 0
94 for line in lines:
95 w = line.split()
96 if line[0].isdigit(): # tabular format
97 chr1, beg1, seqlen1 = w[1], int(w[2]), int(w[5])
98 if w[4] == "-": beg1 -= seqlen1
99 chr2, beg2, seqlen2 = w[6], int(w[7]), int(w[10])
100 if w[9] == "-": beg2 -= seqlen2
101 blocks = tabBlocks(beg1, beg2, w[11])
102 yield chr1, seqlen1, chr2, seqlen2, blocks
103 elif line[0] == "s": # MAF format
104 if mafCount == 0:
105 chr1, beg1, seqlen1, seq1 = w[1], int(w[2]), int(w[5]), w[6]
106 if w[4] == "-": beg1 -= seqlen1
107 mafCount = 1
108 else:
109 chr2, beg2, seqlen2, seq2 = w[1], int(w[2]), int(w[5]), w[6]
110 if w[4] == "-": beg2 -= seqlen2
111 blocks = mafBlocks(beg1, beg2, seq1, seq2)
112 yield chr1, seqlen1, chr2, seqlen2, blocks
113 mafCount = 0
114
115 def readAlignments(lines):
116 '''Get alignments and sequence lengths, from MAF or tabular format.'''
117 alignments = []
118 seqLengths1 = {}
119 seqLengths2 = {}
120 for chr1, seqlen1, chr2, seqlen2, blocks in alignmentInput(lines):
121 aln = chr1, chr2, blocks
122 alignments.append(aln)
123 seqLengths1[chr1] = seqlen1
124 seqLengths2[chr2] = seqlen2
125 return alignments, seqLengths1, seqLengths2
126
127 sys.stderr.write(my_name + ": reading alignments...\n")
128 input = fileinput.input(args[0])
129 alignments, seq_size_dic1, seq_size_dic2 = readAlignments(input)
130 sys.stderr.write(my_name + ": done\n")
131
132 if not alignments:
133 sys.exit(my_name + ": there are no alignments")
134
135 def natural_sort_key(my_string):
136 '''Return a sort key for "natural" ordering, e.g. chr9 < chr10.'''
137 parts = re.split(r'(\d+)', my_string)
138 parts[1::2] = map(int, parts[1::2])
139 return parts
140
141 def get_text_sizes(my_strings):
142 '''Get widths & heights, in pixels, of some strings.'''
143 if opts.fontsize == 0: return [(0, 0) for i in my_strings]
144 image_size = 1, 1
145 im = Image.new(image_mode, image_size)
146 draw = ImageDraw.Draw(im)
147 return [draw.textsize(i, font=font) for i in my_strings]
148
149 def get_seq_info(seq_size_dic):
150 '''Return miscellaneous information about the sequences.'''
151 seq_names = seq_size_dic.keys()
152 seq_names.sort(key=natural_sort_key)
153 seq_sizes = [seq_size_dic[i] for i in seq_names]
154 name_sizes = get_text_sizes(seq_names)
155 margin = max(zip(*name_sizes)[1]) # maximum text height
156 return seq_names, seq_sizes, name_sizes, margin
157
158 seq_names1, seq_sizes1, name_sizes1, margin1 = get_seq_info(seq_size_dic1)
159 seq_names2, seq_sizes2, name_sizes2, margin2 = get_seq_info(seq_size_dic2)
160
161 def div_ceil(x, y):
162 '''Return x / y rounded up.'''
163 q, r = divmod(x, y)
164 return q + (r != 0)
165
166 def tot_seq_pix(seq_sizes, bp_per_pix):
167 '''Return the total pixels needed for sequences of the given sizes.'''
168 return sum([div_ceil(i, bp_per_pix) for i in seq_sizes])
169
170 def get_bp_per_pix(seq_sizes, pix_limit):
171 '''Get the minimum bp-per-pixel that fits in the size limit.'''
172 seq_num = len(seq_sizes)
173 seq_pix_limit = pix_limit - pix_tween_seqs * (seq_num - 1)
174 if seq_pix_limit < seq_num:
175 sys.exit(my_name + ": can't fit the image: too many sequences?")
176 lower_bound = div_ceil(sum(seq_sizes), seq_pix_limit)
177 for bp_per_pix in itertools.count(lower_bound): # slow linear search
178 if tot_seq_pix(seq_sizes, bp_per_pix) <= seq_pix_limit: break
179 return bp_per_pix
180
181 sys.stderr.write(my_name + ": choosing bp per pixel...\n")
182 bp_per_pix1 = get_bp_per_pix(seq_sizes1, opts.width - margin1)
183 bp_per_pix2 = get_bp_per_pix(seq_sizes2, opts.height - margin2)
184 bp_per_pix = max(bp_per_pix1, bp_per_pix2)
185 sys.stderr.write(my_name + ": bp per pixel = " + str(bp_per_pix) + "\n")
186
187 def get_seq_starts(seq_pix, pix_tween_seqs, margin):
188 '''Get the start pixel for each sequence.'''
189 seq_starts = []
190 pix_tot = margin - pix_tween_seqs
191 for i in seq_pix:
192 pix_tot += pix_tween_seqs
193 seq_starts.append(pix_tot)
194 pix_tot += i
195 return seq_starts
196
197 def get_pix_info(seq_sizes, margin):
198 '''Return pixel information about the sequences.'''
199 seq_pix = [div_ceil(i, bp_per_pix) for i in seq_sizes]
200 seq_starts = get_seq_starts(seq_pix, pix_tween_seqs, margin)
201 tot_pix = seq_starts[-1] + seq_pix[-1]
202 return seq_pix, seq_starts, tot_pix
203
204 seq_pix1, seq_starts1, width = get_pix_info(seq_sizes1, margin1)
205 seq_pix2, seq_starts2, height = get_pix_info(seq_sizes2, margin2)
206 seq_start_dic1 = dict(zip(seq_names1, seq_starts1))
207 seq_start_dic2 = dict(zip(seq_names2, seq_starts2))
208 hits = [0] * (width * height) # the image data
209
210 sys.stderr.write(my_name + ": processing alignments...\n")
211 for seq1, seq2, blocks in alignments:
212 seq_start1 = seq_start_dic1[seq1]
213 seq_start2 = seq_start_dic2[seq2]
214 my_start = seq_start2 * width + seq_start1
215 for beg1, beg2, size in blocks:
216 end1 = beg1 + size
217 end2 = beg2 + size
218 if beg1 >= 0: j = xrange(beg1, end1)
219 else: j = xrange(-1 - beg1, -1 - end1, -1)
220 if beg2 >= 0: k = xrange(beg2, end2)
221 else: k = xrange(-1 - beg2, -1 - end2, -1)
222 if beg2 >= 0: store_value = 1
223 else: store_value = 2
224 for real_pos1, real_pos2 in itertools.izip(j, k):
225 pix1 = real_pos1 // bp_per_pix
226 pix2 = real_pos2 // bp_per_pix
227 hits[my_start + pix2 * width + pix1] |= store_value
228 sys.stderr.write(my_name + ": done\n")
229
230 def make_label(text, text_size, range_start, range_size):
231 '''Return an axis label with endpoint & sort-order information.'''
232 text_width = text_size[0]
233 label_start = range_start + (range_size - text_width) // 2
234 label_end = label_start + text_width
235 sort_key = text_width - range_size
236 return sort_key, label_start, label_end, text
237
238 def get_nonoverlapping_labels(labels):
239 '''Get a subset of non-overlapping axis labels, greedily.'''
240 nonoverlapping_labels = []
241 for i in labels:
242 if True not in [i[1] < j[2] + label_space and j[1] < i[2] + label_space
243 for j in nonoverlapping_labels]:
244 nonoverlapping_labels.append(i)
245 return nonoverlapping_labels
246
247 def get_axis_image(seq_names, name_sizes, seq_starts, seq_pix):
248 '''Make an image of axis labels.'''
249 min_pos = seq_starts[0]
250 max_pos = seq_starts[-1] + seq_pix[-1]
251 height = max(zip(*name_sizes)[1])
252 labels = [make_label(i, j, k, l) for i, j, k, l in
253 zip(seq_names, name_sizes, seq_starts, seq_pix)]
254 labels = [i for i in labels if i[1] >= min_pos and i[2] <= max_pos]
255 labels.sort()
256 labels = get_nonoverlapping_labels(labels)
257 image_size = max_pos, height
258 im = Image.new(image_mode, image_size, border_shade)
259 draw = ImageDraw.Draw(im)
260 for i in labels:
261 position = i[1], 0
262 draw.text(position, i[3], font=font, fill=text_color)
263 return im
264
265 image_size = width, height
266 im = Image.new(image_mode, image_size, background_color)
267
268 for i in range(height):
269 for j in range(width):
270 store_value = hits[i * width + j]
271 xy = j, i
272 if store_value == 1: im.putpixel(xy, forward_color)
273 elif store_value == 2: im.putpixel(xy, reverse_color)
274 elif store_value == 3: im.putpixel(xy, overlap_color)
275
276 if opts.fontsize != 0:
277 axis1 = get_axis_image(seq_names1, name_sizes1, seq_starts1, seq_pix1)
278 axis2 = get_axis_image(seq_names2, name_sizes2, seq_starts2, seq_pix2)
279 axis2 = axis2.rotate(270)
280 im.paste(axis1, (0, 0))
281 im.paste(axis2, (0, 0))
282
283 for i in seq_starts1[1:]:
284 box = i - pix_tween_seqs, margin2, i, height
285 im.paste(border_shade, box)
286
287 for i in seq_starts2[1:]:
288 box = margin1, i - pix_tween_seqs, width, i
289 im.paste(border_shade, box)
290
291 im.save(args[1])