scripts/last-dotplot
author Martin C. Frith
Mon Oct 19 12:25:49 2015 +0900 (2015-10-19)
changeset 647 25c8084d7f6e
parent 646 504ecca38a3e
child 648 33e285b3e428
permissions -rwxr-xr-x
Refactoring.
     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 def warn(message):
    19     prog = os.path.basename(sys.argv[0])
    20     sys.stderr.write(prog + ": " + message + "\n")
    21 
    22 def tabBlocks(beg1, beg2, blocks):
    23     '''Get the gapless blocks of an alignment, from LAST tabular format.'''
    24     for i in blocks.split(","):
    25         if ":" in i:
    26             x, y = i.split(":")
    27             beg1 += int(x)
    28             beg2 += int(y)
    29         else:
    30             size = int(i)
    31             yield beg1, beg2, size
    32             beg1 += size
    33             beg2 += size
    34 
    35 def mafBlocks(beg1, beg2, seq1, seq2):
    36     '''Get the gapless blocks of an alignment, from MAF format.'''
    37     size = 0
    38     for x, y in itertools.izip(seq1, seq2):
    39         if x == "-":
    40             if size:
    41                 yield beg1, beg2, size
    42                 beg1 += size
    43                 beg2 += size
    44                 size = 0
    45             beg2 += 1
    46         elif y == "-":
    47             if size:
    48                 yield beg1, beg2, size
    49                 beg1 += size
    50                 beg2 += size
    51                 size = 0
    52             beg1 += 1
    53         else:
    54             size += 1
    55     if size: yield beg1, beg2, size
    56 
    57 def alignmentInput(lines):
    58     '''Get alignments and sequence lengths, from MAF or tabular format.'''
    59     mafCount = 0
    60     for line in lines:
    61         w = line.split()
    62         if line[0].isdigit():  # tabular format
    63             chr1, beg1, seqlen1 = w[1], int(w[2]), int(w[5])
    64             if w[4] == "-": beg1 -= seqlen1
    65             chr2, beg2, seqlen2 = w[6], int(w[7]), int(w[10])
    66             if w[9] == "-": beg2 -= seqlen2
    67             blocks = tabBlocks(beg1, beg2, w[11])
    68             yield chr1, seqlen1, chr2, seqlen2, blocks
    69         elif line[0] == "s":  # MAF format
    70             if mafCount == 0:
    71                 chr1, beg1, seqlen1, seq1 = w[1], int(w[2]), int(w[5]), w[6]
    72                 if w[4] == "-": beg1 -= seqlen1
    73                 mafCount = 1
    74             else:
    75                 chr2, beg2, seqlen2, seq2 = w[1], int(w[2]), int(w[5]), w[6]
    76                 if w[4] == "-": beg2 -= seqlen2
    77                 blocks = mafBlocks(beg1, beg2, seq1, seq2)
    78                 yield chr1, seqlen1, chr2, seqlen2, blocks
    79                 mafCount = 0
    80 
    81 def readAlignments(lines):
    82     '''Get alignments and sequence lengths, from MAF or tabular format.'''
    83     alignments = []
    84     seqLengths1 = {}
    85     seqLengths2 = {}
    86     for chr1, seqlen1, chr2, seqlen2, blocks in alignmentInput(lines):
    87         aln = chr1, chr2, blocks
    88         alignments.append(aln)
    89         seqLengths1[chr1] = seqlen1
    90         seqLengths2[chr2] = seqlen2
    91     return alignments, seqLengths1, seqLengths2
    92 
    93 def natural_sort_key(my_string):
    94     '''Return a sort key for "natural" ordering, e.g. chr9 < chr10.'''
    95     parts = re.split(r'(\d+)', my_string)
    96     parts[1::2] = map(int, parts[1::2])
    97     return parts
    98 
    99 def get_text_sizes(my_strings, font, fontsize, image_mode):
   100     '''Get widths & heights, in pixels, of some strings.'''
   101     if fontsize == 0: return [(0, 0) for i in my_strings]
   102     image_size = 1, 1
   103     im = Image.new(image_mode, image_size)
   104     draw = ImageDraw.Draw(im)
   105     return [draw.textsize(i, font=font) for i in my_strings]
   106 
   107 def get_seq_info(seq_size_dic, font, fontsize, image_mode):
   108     '''Return miscellaneous information about the sequences.'''
   109     seq_names = seq_size_dic.keys()
   110     seq_names.sort(key=natural_sort_key)
   111     seq_sizes = [seq_size_dic[i] for i in seq_names]
   112     name_sizes = get_text_sizes(seq_names, font, fontsize, image_mode)
   113     margin = max(zip(*name_sizes)[1])  # maximum text height
   114     return seq_names, seq_sizes, name_sizes, margin
   115 
   116 def div_ceil(x, y):
   117     '''Return x / y rounded up.'''
   118     q, r = divmod(x, y)
   119     return q + (r != 0)
   120 
   121 def tot_seq_pix(seq_sizes, bp_per_pix):
   122     '''Return the total pixels needed for sequences of the given sizes.'''
   123     return sum([div_ceil(i, bp_per_pix) for i in seq_sizes])
   124 
   125 def get_bp_per_pix(seq_sizes, pix_tween_seqs, pix_limit):
   126     '''Get the minimum bp-per-pixel that fits in the size limit.'''
   127     seq_num = len(seq_sizes)
   128     seq_pix_limit = pix_limit - pix_tween_seqs * (seq_num - 1)
   129     if seq_pix_limit < seq_num:
   130         sys.exit(my_name + ": can't fit the image: too many sequences?")
   131     lower_bound = div_ceil(sum(seq_sizes), seq_pix_limit)
   132     for bp_per_pix in itertools.count(lower_bound):  # slow linear search
   133         if tot_seq_pix(seq_sizes, bp_per_pix) <= seq_pix_limit: break
   134     return bp_per_pix
   135 
   136 def get_seq_starts(seq_pix, pix_tween_seqs, margin):
   137     '''Get the start pixel for each sequence.'''
   138     seq_starts = []
   139     pix_tot = margin - pix_tween_seqs
   140     for i in seq_pix:
   141         pix_tot += pix_tween_seqs
   142         seq_starts.append(pix_tot)
   143         pix_tot += i
   144     return seq_starts
   145 
   146 def get_pix_info(seq_sizes, bp_per_pix, pix_tween_seqs, margin):
   147     '''Return pixel information about the sequences.'''
   148     seq_pix = [div_ceil(i, bp_per_pix) for i in seq_sizes]
   149     seq_starts = get_seq_starts(seq_pix, pix_tween_seqs, margin)
   150     tot_pix = seq_starts[-1] + seq_pix[-1]
   151     return seq_pix, seq_starts, tot_pix
   152 
   153 def drawLineForward(hits, width, bp_per_pix, origin, beg1, beg2, size):
   154     while True:
   155         q1, r1 = divmod(beg1, bp_per_pix)
   156         q2, r2 = divmod(beg2, bp_per_pix)
   157         hits[origin + q2 * width + q1] |= 1
   158         next_pix = min(bp_per_pix - r1, bp_per_pix - r2)
   159         if next_pix >= size: break
   160         beg1 += next_pix
   161         beg2 += next_pix
   162         size -= next_pix
   163 
   164 def drawLineReverse(hits, width, bp_per_pix, origin, beg1, beg2, size):
   165     beg2 = -1 - beg2
   166     while True:
   167         q1, r1 = divmod(beg1, bp_per_pix)
   168         q2, r2 = divmod(beg2, bp_per_pix)
   169         hits[origin + q2 * width + q1] |= 2
   170         next_pix = min(bp_per_pix - r1, r2 + 1)
   171         if next_pix >= size: break
   172         beg1 += next_pix
   173         beg2 -= next_pix
   174         size -= next_pix
   175 
   176 def alignmentPixels(width, height, alignments, bp_per_pix,
   177                     seq_start_dic1, seq_start_dic2):
   178     hits = [0] * (width * height)  # the image data
   179     for seq1, seq2, blocks in alignments:
   180         seq_start1 = seq_start_dic1[seq1]
   181         seq_start2 = seq_start_dic2[seq2]
   182         origin = seq_start2 * width + seq_start1
   183         for beg1, beg2, size in blocks:
   184             if beg1 < 0:
   185                 beg1 = -(beg1 + size)
   186                 beg2 = -(beg2 + size)
   187             if beg2 >= 0:
   188                 drawLineForward(hits, width, bp_per_pix, origin,
   189                                 beg1, beg2, size)
   190             else:
   191                 drawLineReverse(hits, width, bp_per_pix, origin,
   192                                 beg1, beg2, size)
   193     return hits
   194 
   195 def make_label(text, text_size, range_start, range_size):
   196     '''Return an axis label with endpoint & sort-order information.'''
   197     text_width  = text_size[0]
   198     label_start = range_start + (range_size - text_width) // 2
   199     label_end   = label_start + text_width
   200     sort_key    = text_width - range_size
   201     return sort_key, label_start, label_end, text
   202 
   203 def get_nonoverlapping_labels(labels, label_space):
   204     '''Get a subset of non-overlapping axis labels, greedily.'''
   205     nonoverlapping_labels = []
   206     for i in labels:
   207         if True not in [i[1] < j[2] + label_space and j[1] < i[2] + label_space
   208                         for j in nonoverlapping_labels]:
   209             nonoverlapping_labels.append(i)
   210     return nonoverlapping_labels
   211 
   212 def get_axis_image(seq_names, name_sizes, seq_starts, seq_pix,
   213                    font, image_mode, opts):
   214     '''Make an image of axis labels.'''
   215     min_pos = seq_starts[0]
   216     max_pos = seq_starts[-1] + seq_pix[-1]
   217     height = max(zip(*name_sizes)[1])
   218     labels = [make_label(i, j, k, l) for i, j, k, l in
   219               zip(seq_names, name_sizes, seq_starts, seq_pix)]
   220     labels = [i for i in labels if i[1] >= min_pos and i[2] <= max_pos]
   221     labels.sort()
   222     labels = get_nonoverlapping_labels(labels, opts.label_space)
   223     image_size = max_pos, height
   224     im = Image.new(image_mode, image_size, opts.border_shade)
   225     draw = ImageDraw.Draw(im)
   226     for i in labels:
   227         position = i[1], 0
   228         draw.text(position, i[3], font=font, fill=opts.text_color)
   229     return im
   230 
   231 if __name__ == "__main__":
   232     my_name = os.path.basename(sys.argv[0])
   233     usage = """
   234   %prog --help
   235   %prog [options] last-tabular-output dotplot.png
   236   %prog [options] last-tabular-output dotplot.gif
   237   etc."""
   238     op = optparse.OptionParser(usage=usage)
   239     # Replace "width" & "height" with a single "length" option?
   240     op.add_option("-x", "--width", type="int", default=1000,
   241                   help="maximum width in pixels (default: %default)")
   242     op.add_option("-y", "--height", type="int", default=1000,
   243                   help="maximum height in pixels (default: %default)")
   244     op.add_option("-f", "--fontfile",
   245                   help="TrueType or OpenType font file")
   246     op.add_option("-s", "--fontsize", type="int", default=11,
   247                   help="TrueType or OpenType font size (default: %default)")
   248     op.add_option("-c", "--forwardcolor", default="red",
   249                   help="Color for forward alignments (default: %default)")
   250     op.add_option("-r", "--reversecolor", default="blue",
   251                   help="Color for reverse alignments (default: %default)")
   252     (opts, args) = op.parse_args()
   253     if len(args) != 2: op.error("2 arguments needed")
   254 
   255     if opts.fontfile:  font = ImageFont.truetype(opts.fontfile, opts.fontsize)
   256     else:              font = ImageFont.load_default()
   257 
   258     opts.text_color = "black"
   259     opts.background_color = "white"
   260     opts.pix_tween_seqs = 2  # number of border pixels between sequences
   261     opts.border_shade = 239, 239, 239  # the shade of grey for border pixels
   262     opts.label_space = 5     # minimum number of pixels between axis labels
   263 
   264     image_mode = 'RGB'
   265     forward_color = ImageColor.getcolor(opts.forwardcolor, image_mode)
   266     reverse_color = ImageColor.getcolor(opts.reversecolor, image_mode)
   267     zipped_colors = zip(forward_color, reverse_color)
   268     overlap_color = tuple([(i + j) // 2 for i, j in zipped_colors])
   269 
   270     warn("reading alignments...")
   271     input = fileinput.input(args[0])
   272     alignments, seq_size_dic1, seq_size_dic2 = readAlignments(input)
   273     warn("done")
   274 
   275     if not alignments:
   276         sys.exit(my_name + ": there are no alignments")
   277 
   278     seq_info1 = get_seq_info(seq_size_dic1, font, opts.fontsize, image_mode)
   279     seq_info2 = get_seq_info(seq_size_dic2, font, opts.fontsize, image_mode)
   280     seq_names1, seq_sizes1, name_sizes1, margin1 = seq_info1
   281     seq_names2, seq_sizes2, name_sizes2, margin2 = seq_info2
   282 
   283     warn("choosing bp per pixel...")
   284     pix_limit1 = opts.width  - margin1
   285     pix_limit2 = opts.height - margin2
   286     bp_per_pix1 = get_bp_per_pix(seq_sizes1, opts.pix_tween_seqs, pix_limit1)
   287     bp_per_pix2 = get_bp_per_pix(seq_sizes2, opts.pix_tween_seqs, pix_limit2)
   288     bp_per_pix = max(bp_per_pix1, bp_per_pix2)
   289     warn("bp per pixel = " + str(bp_per_pix))
   290 
   291     seq_pix1, seq_starts1, width  = get_pix_info(seq_sizes1, bp_per_pix,
   292                                                  opts.pix_tween_seqs, margin1)
   293     seq_pix2, seq_starts2, height = get_pix_info(seq_sizes2, bp_per_pix,
   294                                                  opts.pix_tween_seqs, margin2)
   295     seq_start_dic1 = dict(zip(seq_names1, seq_starts1))
   296     seq_start_dic2 = dict(zip(seq_names2, seq_starts2))
   297 
   298     warn("processing alignments...")
   299     hits = alignmentPixels(width, height, alignments, bp_per_pix,
   300                            seq_start_dic1, seq_start_dic2)
   301     warn("done")
   302 
   303     image_size = width, height
   304     im = Image.new(image_mode, image_size, opts.background_color)
   305 
   306     for i in range(height):
   307         for j in range(width):
   308             store_value = hits[i * width + j]
   309             xy = j, i
   310             if   store_value == 1: im.putpixel(xy, forward_color)
   311             elif store_value == 2: im.putpixel(xy, reverse_color)
   312             elif store_value == 3: im.putpixel(xy, overlap_color)
   313 
   314     if opts.fontsize != 0:
   315         axis1 = get_axis_image(seq_names1, name_sizes1, seq_starts1, seq_pix1,
   316                                font, image_mode, opts)
   317         axis2 = get_axis_image(seq_names2, name_sizes2, seq_starts2, seq_pix2,
   318                                font, image_mode, opts)
   319         axis2 = axis2.rotate(270)
   320         im.paste(axis1, (0, 0))
   321         im.paste(axis2, (0, 0))
   322 
   323     for i in seq_starts1[1:]:
   324         box = i - opts.pix_tween_seqs, margin2, i, height
   325         im.paste(opts.border_shade, box)
   326 
   327     for i in seq_starts2[1:]:
   328         box = margin1, i - opts.pix_tween_seqs, width, i
   329         im.paste(opts.border_shade, box)
   330 
   331     im.save(args[1])