scripts/last-dotplot
author Martin C. Frith
Tue Apr 04 12:15:35 2017 +0900 (2017-04-04)
changeset 846 1f46ab956351
parent 845 16060c00b129
child 847 3ca7aa4b27a8
permissions -rwxr-xr-x
Added last-dotplot options to show sequence lengths.
     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 fnmatch, 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 myOpen(fileName):  # faster than fileinput
    19     if fileName == "-":
    20         return sys.stdin
    21     return open(fileName)
    22 
    23 def warn(message):
    24     prog = os.path.basename(sys.argv[0])
    25     sys.stderr.write(prog + ": " + message + "\n")
    26 
    27 def croppedBlocks(blocks, range1, range2):
    28     cropBeg1, cropEnd1 = range1
    29     cropBeg2, cropEnd2 = range2
    30     if blocks[0][0] < 0: cropBeg1, cropEnd1 = -cropEnd1, -cropBeg1
    31     if blocks[0][1] < 0: cropBeg2, cropEnd2 = -cropEnd2, -cropBeg2
    32     for beg1, beg2, size in blocks:
    33         b1 = max(cropBeg1, beg1)
    34         e1 = min(cropEnd1, beg1 + size)
    35         if b1 >= e1: continue
    36         offset = beg2 - beg1
    37         b2 = max(cropBeg2, b1 + offset)
    38         e2 = min(cropEnd2, e1 + offset)
    39         if b2 >= e2: continue
    40         yield b2 - offset, b2, e2 - b2
    41 
    42 def tabBlocks(beg1, beg2, blocks):
    43     '''Get the gapless blocks of an alignment, from LAST tabular format.'''
    44     for i in blocks.split(","):
    45         if ":" in i:
    46             x, y = i.split(":")
    47             beg1 += int(x)
    48             beg2 += int(y)
    49         else:
    50             size = int(i)
    51             yield beg1, beg2, size
    52             beg1 += size
    53             beg2 += size
    54 
    55 def mafBlocks(beg1, beg2, seq1, seq2):
    56     '''Get the gapless blocks of an alignment, from MAF format.'''
    57     size = 0
    58     for x, y in itertools.izip(seq1, seq2):
    59         if x == "-":
    60             if size:
    61                 yield beg1, beg2, size
    62                 beg1 += size
    63                 beg2 += size
    64                 size = 0
    65             beg2 += 1
    66         elif y == "-":
    67             if size:
    68                 yield beg1, beg2, size
    69                 beg1 += size
    70                 beg2 += size
    71                 size = 0
    72             beg1 += 1
    73         else:
    74             size += 1
    75     if size: yield beg1, beg2, size
    76 
    77 def alignmentInput(lines):
    78     '''Get alignments and sequence lengths, from MAF or tabular format.'''
    79     mafCount = 0
    80     for line in lines:
    81         w = line.split()
    82         if line[0].isdigit():  # tabular format
    83             chr1, beg1, seqlen1 = w[1], int(w[2]), int(w[5])
    84             if w[4] == "-": beg1 -= seqlen1
    85             chr2, beg2, seqlen2 = w[6], int(w[7]), int(w[10])
    86             if w[9] == "-": beg2 -= seqlen2
    87             blocks = list(tabBlocks(beg1, beg2, w[11]))
    88             yield chr1, seqlen1, chr2, seqlen2, blocks
    89         elif line[0] == "s":  # MAF format
    90             if mafCount == 0:
    91                 chr1, beg1, seqlen1, seq1 = w[1], int(w[2]), int(w[5]), w[6]
    92                 if w[4] == "-": beg1 -= seqlen1
    93                 mafCount = 1
    94             else:
    95                 chr2, beg2, seqlen2, seq2 = w[1], int(w[2]), int(w[5]), w[6]
    96                 if w[4] == "-": beg2 -= seqlen2
    97                 blocks = list(mafBlocks(beg1, beg2, seq1, seq2))
    98                 yield chr1, seqlen1, chr2, seqlen2, blocks
    99                 mafCount = 0
   100 
   101 def seqRangeFromText(text):
   102     if ":" in text:
   103         pattern, interval = text.rsplit(":", 1)
   104         if "-" in interval:
   105             beg, end = interval.rsplit("-", 1)
   106             return pattern, int(beg), int(end)  # beg may be negative
   107     return text, 0, sys.maxsize
   108 
   109 def rangeFromSeqName(seqRanges, name, seqLen):
   110     if not seqRanges: return 0, seqLen
   111     base = name.split(".")[-1]  # allow for names like hg19.chr7
   112     for pat, beg, end in seqRanges:
   113         if fnmatch.fnmatchcase(name, pat) or fnmatch.fnmatchcase(base, pat):
   114             return max(beg, 0), min(end, seqLen)
   115     return None
   116 
   117 def updateSeqLimits(isTrim, seqLimits, seqName, seqRange, blocks, index):
   118     if isTrim:
   119         beg = blocks[0][index]
   120         end = blocks[-1][index] + blocks[-1][2]
   121         if beg < 0: beg, end = -end, -beg
   122         if seqName in seqLimits:
   123             b, e = seqLimits[seqName]
   124             seqLimits[seqName] = min(b, beg), max(e, end)
   125         else:
   126             seqLimits[seqName] = beg, end
   127     else:
   128         seqLimits[seqName] = seqRange
   129 
   130 def readAlignments(fileName, opts):
   131     '''Get alignments and sequence limits, from MAF or tabular format.'''
   132     seqRanges1 = map(seqRangeFromText, opts.seq1)
   133     seqRanges2 = map(seqRangeFromText, opts.seq2)
   134 
   135     alignments = []
   136     seqLimits1 = {}
   137     seqLimits2 = {}
   138     lines = myOpen(fileName)
   139     for seqName1, seqLen1, seqName2, seqLen2, blocks in alignmentInput(lines):
   140         range1 = rangeFromSeqName(seqRanges1, seqName1, seqLen1)
   141         if not range1: continue
   142         range2 = rangeFromSeqName(seqRanges2, seqName2, seqLen2)
   143         if not range2: continue
   144         b = list(croppedBlocks(blocks, range1, range2))
   145         if not b: continue
   146         aln = seqName1, seqName2, b
   147         alignments.append(aln)
   148         updateSeqLimits(opts.trim1, seqLimits1, seqName1, range1, b, 0)
   149         updateSeqLimits(opts.trim2, seqLimits2, seqName2, range2, b, 1)
   150     return alignments, seqLimits1, seqLimits2
   151 
   152 def natural_sort_key(my_string):
   153     '''Return a sort key for "natural" ordering, e.g. chr9 < chr10.'''
   154     parts = re.split(r'(\d+)', my_string)
   155     parts[1::2] = map(int, parts[1::2])
   156     return parts
   157 
   158 def get_text_sizes(my_strings, font, fontsize, image_mode):
   159     '''Get widths & heights, in pixels, of some strings.'''
   160     if fontsize == 0: return [(0, 0) for i in my_strings]
   161     image_size = 1, 1
   162     im = Image.new(image_mode, image_size)
   163     draw = ImageDraw.Draw(im)
   164     return [draw.textsize(i, font=font) for i in my_strings]
   165 
   166 def sizeText(size):
   167     suffixes = "bp", "kb", "Mb", "Gb"
   168     for i, x in enumerate(suffixes):
   169         j = 10 ** (i * 3)
   170         if size < j * 10:
   171             return "%.2g" % (1.0 * size / j) + x
   172         if size < j * 1000 or i == len(suffixes) - 1:
   173             return "%.0f" % (1.0 * size / j) + x
   174 
   175 def seqNameAndSizeText(seqName, seqSize):
   176     return seqName + ": " + sizeText(seqSize)
   177 
   178 def getSeqInfo(seqLimits, font, fontsize, image_mode, isShowSize):
   179     '''Return miscellaneous information about the sequences.'''
   180     seqNames = seqLimits.keys()
   181     seqNames.sort(key=natural_sort_key)
   182     seq_sizes = [seqLimits[i][1] - seqLimits[i][0] for i in seqNames]
   183     if isShowSize: seqLabels = map(seqNameAndSizeText, seqNames, seq_sizes)
   184     else:          seqLabels = seqNames
   185     labelSizes = get_text_sizes(seqLabels, font, fontsize, image_mode)
   186     margin = max(zip(*labelSizes)[1])  # maximum text height
   187     return seqNames, seq_sizes, seqLabels, labelSizes, margin
   188 
   189 def div_ceil(x, y):
   190     '''Return x / y rounded up.'''
   191     q, r = divmod(x, y)
   192     return q + (r != 0)
   193 
   194 def tot_seq_pix(seq_sizes, bp_per_pix):
   195     '''Return the total pixels needed for sequences of the given sizes.'''
   196     return sum([div_ceil(i, bp_per_pix) for i in seq_sizes])
   197 
   198 def get_bp_per_pix(seq_sizes, pix_tween_seqs, pix_limit):
   199     '''Get the minimum bp-per-pixel that fits in the size limit.'''
   200     seq_num = len(seq_sizes)
   201     seq_pix_limit = pix_limit - pix_tween_seqs * (seq_num - 1)
   202     if seq_pix_limit < seq_num:
   203         raise Exception("can't fit the image: too many sequences?")
   204     lower_bound = div_ceil(sum(seq_sizes), seq_pix_limit)
   205     for bp_per_pix in itertools.count(lower_bound):  # slow linear search
   206         if tot_seq_pix(seq_sizes, bp_per_pix) <= seq_pix_limit: break
   207     return bp_per_pix
   208 
   209 def get_seq_starts(seq_pix, pix_tween_seqs, margin):
   210     '''Get the start pixel for each sequence.'''
   211     seq_starts = []
   212     pix_tot = margin - pix_tween_seqs
   213     for i in seq_pix:
   214         pix_tot += pix_tween_seqs
   215         seq_starts.append(pix_tot)
   216         pix_tot += i
   217     return seq_starts
   218 
   219 def get_pix_info(seq_sizes, bp_per_pix, pix_tween_seqs, margin):
   220     '''Return pixel information about the sequences.'''
   221     seq_pix = [div_ceil(i, bp_per_pix) for i in seq_sizes]
   222     seq_starts = get_seq_starts(seq_pix, pix_tween_seqs, margin)
   223     tot_pix = seq_starts[-1] + seq_pix[-1]
   224     return seq_pix, seq_starts, tot_pix
   225 
   226 def drawLineForward(hits, width, bp_per_pix, beg1, beg2, size):
   227     while True:
   228         q1, r1 = divmod(beg1, bp_per_pix)
   229         q2, r2 = divmod(beg2, bp_per_pix)
   230         hits[q2 * width + q1] |= 1
   231         next_pix = min(bp_per_pix - r1, bp_per_pix - r2)
   232         if next_pix >= size: break
   233         beg1 += next_pix
   234         beg2 += next_pix
   235         size -= next_pix
   236 
   237 def drawLineReverse(hits, width, bp_per_pix, beg1, beg2, size):
   238     beg2 = -1 - beg2
   239     while True:
   240         q1, r1 = divmod(beg1, bp_per_pix)
   241         q2, r2 = divmod(beg2, bp_per_pix)
   242         hits[q2 * width + q1] |= 2
   243         next_pix = min(bp_per_pix - r1, r2 + 1)
   244         if next_pix >= size: break
   245         beg1 += next_pix
   246         beg2 -= next_pix
   247         size -= next_pix
   248 
   249 def alignmentPixels(width, height, alignments, bp_per_pix, origins1, origins2):
   250     hits = [0] * (width * height)  # the image data
   251     for seq1, seq2, blocks in alignments:
   252         ori1 = origins1[seq1]
   253         ori2 = origins2[seq2]
   254         for beg1, beg2, size in blocks:
   255             if beg1 < 0:
   256                 beg1 = -(beg1 + size)
   257                 beg2 = -(beg2 + size)
   258             if beg2 >= 0:
   259                 drawLineForward(hits, width, bp_per_pix,
   260                                 beg1 + ori1, beg2 + ori2, size)
   261             else:
   262                 drawLineReverse(hits, width, bp_per_pix,
   263                                 beg1 + ori1, beg2 - ori2, size)
   264     return hits
   265 
   266 def expandedSeqDict(seqDict):
   267     '''Allow lookup by short sequence names, e.g. chr7 as well as hg19.chr7.'''
   268     newDict = {}
   269     for name, x in seqDict.items():
   270         base = name.split(".")[-1]
   271         newDict[name] = x
   272         newDict[base] = x
   273     return newDict
   274 
   275 def readBed(fileName, seqLimits):
   276     if not fileName: return
   277     for line in myOpen(fileName):
   278         w = line.split()
   279         if not w or w[0][0] == "#": continue
   280         seqName = w[0]
   281         if seqName not in seqLimits: continue
   282         cropBeg, cropEnd = seqLimits[seqName]
   283         beg = int(w[1])
   284         end = int(w[2])
   285         b = max(beg, cropBeg)
   286         e = min(end, cropEnd)
   287         if b >= e: continue
   288         if len(w) > 8:
   289             color = tuple(map(int, w[8].split(",")))
   290         elif len(w) > 5:
   291             if   w[5] == "+": color = 255, 244, 244
   292             elif w[5] == "-": color = 244, 244, 255
   293             else:             color = 255, 228, 255
   294         else:
   295             color = 255, 228, 255
   296         yield seqName, b, e, color
   297 
   298 def isExtraFirstGapField(fields):
   299     return fields[4].isdigit()
   300 
   301 def readGaps(fileName, seqLimits):
   302     '''Read locations of unsequenced gaps, from an agp or gap file.'''
   303     if not fileName: return
   304     for line in myOpen(fileName):
   305         w = line.split()
   306         if not w or w[0][0] == "#": continue
   307         if isExtraFirstGapField(w): w = w[1:]
   308         if w[4] not in "NU": continue
   309         seqName = w[0]
   310         if seqName not in seqLimits: continue
   311         cropBeg, cropEnd = seqLimits[seqName]
   312         end = int(w[2])
   313         beg = end - int(w[5])  # zero-based coordinate
   314         b = max(beg, cropBeg)
   315         e = min(end, cropEnd)
   316         if b >= e: continue
   317         bridgedText = w[7]
   318         yield seqName, b, e, bridgedText
   319 
   320 def drawAnnotations(im, beds, origins, margin, limit, isTop, bp_per_pix):
   321     # XXX no consideration of different-color overlaps
   322     for seqName, beg, end, color in beds:
   323         ori = origins[seqName]
   324         b = (ori + beg) // bp_per_pix
   325         e = div_ceil(ori + end, bp_per_pix)
   326         if isTop: box = b, margin, e, limit
   327         else:     box = margin, b, limit, e
   328         im.paste(color, box)
   329 
   330 def drawUnsequencedGaps(im, gaps, origins, margin, limit, isTop, bridgedText,
   331                         bp_per_pix, color):
   332     '''Draw rectangles representing unsequenced gaps.'''
   333     for seqName, beg, end, b in gaps:
   334         if b != bridgedText: continue
   335         ori = origins[seqName]
   336         b = div_ceil(ori + beg, bp_per_pix)  # use fully-covered pixels only
   337         e = (ori + end) // bp_per_pix
   338         if e <= b: continue
   339         if isTop: box = b, margin, e, limit
   340         else:     box = margin, b, limit, e
   341         im.paste(color, box)
   342 
   343 def make_label(text, text_size, range_start, range_size):
   344     '''Return an axis label with endpoint & sort-order information.'''
   345     text_width  = text_size[0]
   346     label_start = range_start + (range_size - text_width) // 2
   347     label_end   = label_start + text_width
   348     sort_key    = text_width - range_size
   349     return sort_key, label_start, label_end, text
   350 
   351 def get_nonoverlapping_labels(labels, label_space):
   352     '''Get a subset of non-overlapping axis labels, greedily.'''
   353     nonoverlapping_labels = []
   354     for i in labels:
   355         if True not in [i[1] < j[2] + label_space and j[1] < i[2] + label_space
   356                         for j in nonoverlapping_labels]:
   357             nonoverlapping_labels.append(i)
   358     return nonoverlapping_labels
   359 
   360 def get_axis_image(seqNames, name_sizes, seq_starts, seq_pix,
   361                    font, image_mode, opts):
   362     '''Make an image of axis labels.'''
   363     min_pos = seq_starts[0]
   364     max_pos = seq_starts[-1] + seq_pix[-1]
   365     height = max(zip(*name_sizes)[1])
   366     labels = [make_label(i, j, k, l) for i, j, k, l in
   367               zip(seqNames, name_sizes, seq_starts, seq_pix)]
   368     labels = [i for i in labels if i[1] >= min_pos and i[2] <= max_pos]
   369     labels.sort()
   370     labels = get_nonoverlapping_labels(labels, opts.label_space)
   371     image_size = max_pos, height
   372     im = Image.new(image_mode, image_size, opts.border_shade)
   373     draw = ImageDraw.Draw(im)
   374     for i in labels:
   375         position = i[1], 0
   376         draw.text(position, i[3], font=font, fill=opts.text_color)
   377     return im
   378 
   379 def seqOrigins(seqNames, seq_starts, seqLimits, bp_per_pix):
   380     for i, j in zip(seqNames, seq_starts):
   381         yield i, bp_per_pix * j - seqLimits[i][0]
   382 
   383 def lastDotplot(opts, args):
   384     if opts.fontfile:  font = ImageFont.truetype(opts.fontfile, opts.fontsize)
   385     else:              font = ImageFont.load_default()
   386 
   387     image_mode = 'RGB'
   388     forward_color = ImageColor.getcolor(opts.forwardcolor, image_mode)
   389     reverse_color = ImageColor.getcolor(opts.reversecolor, image_mode)
   390     zipped_colors = zip(forward_color, reverse_color)
   391     overlap_color = tuple([(i + j) // 2 for i, j in zipped_colors])
   392 
   393     warn("reading alignments...")
   394     alignments, seqLimits1, seqLimits2 = readAlignments(args[0], opts)
   395     warn("done")
   396 
   397     if not alignments: raise Exception("there are no alignments")
   398 
   399     i1 = getSeqInfo(seqLimits1, font, opts.fontsize, image_mode, opts.lengths1)
   400     seqNames1, seq_sizes1, seqLabels1, labelSizes1, margin1 = i1
   401 
   402     i2 = getSeqInfo(seqLimits2, font, opts.fontsize, image_mode, opts.lengths2)
   403     seqNames2, seq_sizes2, seqLabels2, labelSizes2, margin2 = i2
   404 
   405     warn("choosing bp per pixel...")
   406     pix_limit1 = opts.width  - margin1
   407     pix_limit2 = opts.height - margin2
   408     bp_per_pix1 = get_bp_per_pix(seq_sizes1, opts.pix_tween_seqs, pix_limit1)
   409     bp_per_pix2 = get_bp_per_pix(seq_sizes2, opts.pix_tween_seqs, pix_limit2)
   410     bp_per_pix = max(bp_per_pix1, bp_per_pix2)
   411     warn("bp per pixel = " + str(bp_per_pix))
   412 
   413     seq_pix1, seq_starts1, width  = get_pix_info(seq_sizes1, bp_per_pix,
   414                                                  opts.pix_tween_seqs, margin1)
   415     seq_pix2, seq_starts2, height = get_pix_info(seq_sizes2, bp_per_pix,
   416                                                  opts.pix_tween_seqs, margin2)
   417 
   418     origins1 = dict(seqOrigins(seqNames1, seq_starts1, seqLimits1, bp_per_pix))
   419     origins2 = dict(seqOrigins(seqNames2, seq_starts2, seqLimits2, bp_per_pix))
   420 
   421     warn("processing alignments...")
   422     hits = alignmentPixels(width, height, alignments, bp_per_pix,
   423                            origins1, origins2)
   424     warn("done")
   425 
   426     image_size = width, height
   427     im = Image.new(image_mode, image_size, opts.background_color)
   428 
   429     seqLimits1 = expandedSeqDict(seqLimits1)
   430     seqLimits2 = expandedSeqDict(seqLimits2)
   431     origins1 = expandedSeqDict(origins1)
   432     origins2 = expandedSeqDict(origins2)
   433 
   434     beds1 = list(readBed(opts.bed1, seqLimits1))
   435     beds2 = list(readBed(opts.bed2, seqLimits2))
   436     drawAnnotations(im, beds1, origins1, margin2, height, True, bp_per_pix)
   437     drawAnnotations(im, beds2, origins2, margin1, width, False, bp_per_pix)
   438 
   439     gaps1 = list(readGaps(opts.gap1, seqLimits1))
   440     gaps2 = list(readGaps(opts.gap2, seqLimits2))
   441     # draw bridged gaps first, then unbridged gaps on top:
   442     drawUnsequencedGaps(im, gaps1, origins1, margin2, height, True, "yes",
   443                         bp_per_pix, opts.bridged_color)
   444     drawUnsequencedGaps(im, gaps2, origins2, margin1, width, False, "yes",
   445                         bp_per_pix, opts.bridged_color)
   446     drawUnsequencedGaps(im, gaps1, origins1, margin2, height, True, "no",
   447                         bp_per_pix, opts.unbridged_color)
   448     drawUnsequencedGaps(im, gaps2, origins2, margin1, width, False, "no",
   449                         bp_per_pix, opts.unbridged_color)
   450 
   451     for i in range(height):
   452         for j in range(width):
   453             store_value = hits[i * width + j]
   454             xy = j, i
   455             if   store_value == 1: im.putpixel(xy, forward_color)
   456             elif store_value == 2: im.putpixel(xy, reverse_color)
   457             elif store_value == 3: im.putpixel(xy, overlap_color)
   458 
   459     if opts.fontsize != 0:
   460         axis1 = get_axis_image(seqLabels1, labelSizes1, seq_starts1, seq_pix1,
   461                                font, image_mode, opts)
   462         axis2 = get_axis_image(seqLabels2, labelSizes2, seq_starts2, seq_pix2,
   463                                font, image_mode, opts)
   464         axis2 = axis2.transpose(Image.ROTATE_270)  # !!! bug hotspot
   465         im.paste(axis1, (0, 0))
   466         im.paste(axis2, (0, 0))
   467 
   468     for i in seq_starts1[1:]:
   469         box = i - opts.pix_tween_seqs, margin2, i, height
   470         im.paste(opts.border_shade, box)
   471 
   472     for i in seq_starts2[1:]:
   473         box = margin1, i - opts.pix_tween_seqs, width, i
   474         im.paste(opts.border_shade, box)
   475 
   476     im.save(args[1])
   477 
   478 if __name__ == "__main__":
   479     usage = """%prog --help
   480    or: %prog [options] maf-or-tab-alignments dotplot.png
   481    or: %prog [options] maf-or-tab-alignments dotplot.gif
   482    or: ..."""
   483     description = "Draw a dotplot of pair-wise sequence alignments in MAF or tabular format."
   484     op = optparse.OptionParser(usage=usage, description=description)
   485     op.add_option("-1", "--seq1", metavar="PATTERN", action="append",
   486                   default=[],
   487                   help="which sequences to show from the 1st genome")
   488     op.add_option("-2", "--seq2", metavar="PATTERN", action="append",
   489                   default=[],
   490                   help="which sequences to show from the 2nd genome")
   491     # Replace "width" & "height" with a single "length" option?
   492     op.add_option("-x", "--width", type="int", default=1000,
   493                   help="maximum width in pixels (default: %default)")
   494     op.add_option("-y", "--height", type="int", default=1000,
   495                   help="maximum height in pixels (default: %default)")
   496     op.add_option("-f", "--fontfile", metavar="FILE",
   497                   help="TrueType or OpenType font file")
   498     op.add_option("-s", "--fontsize", metavar="SIZE", type="int", default=11,
   499                   help="TrueType or OpenType font size (default: %default)")
   500     op.add_option("-c", "--forwardcolor", metavar="COLOR", default="red",
   501                   help="color for forward alignments (default: %default)")
   502     op.add_option("-r", "--reversecolor", metavar="COLOR", default="blue",
   503                   help="color for reverse alignments (default: %default)")
   504     op.add_option("--trim1", action="store_true",
   505                   help="trim unaligned sequence flanks from the 1st genome")
   506     op.add_option("--trim2", action="store_true",
   507                   help="trim unaligned sequence flanks from the 2nd genome")
   508     op.add_option("--lengths1", action="store_true",
   509                   help="show sequence lengths for the 1st genome")
   510     op.add_option("--lengths2", action="store_true",
   511                   help="show sequence lengths for the 2nd genome")
   512     op.add_option("--bed1", metavar="FILE",
   513                   help="read genome1 annotations from bed file")
   514     op.add_option("--bed2", metavar="FILE",
   515                   help="read genome2 annotations from bed file")
   516 
   517     og = optparse.OptionGroup(op, "Unsequenced gap options")
   518     og.add_option("--gap1", metavar="FILE",
   519                   help="read genome1 unsequenced gaps from agp or gap file")
   520     og.add_option("--gap2", metavar="FILE",
   521                   help="read genome2 unsequenced gaps from agp or gap file")
   522     og.add_option("--bridged-color", metavar="COLOR", default="yellow",
   523                   help="color for bridged gaps (default: %default)")
   524     og.add_option("--unbridged-color", metavar="COLOR", default="pink",
   525                   help="color for unbridged gaps (default: %default)")
   526     op.add_option_group(og)
   527     (opts, args) = op.parse_args()
   528     if len(args) != 2: op.error("2 arguments needed")
   529 
   530     opts.text_color = "black"
   531     opts.background_color = "white"
   532     opts.pix_tween_seqs = 2  # number of border pixels between sequences
   533     opts.border_shade = 239, 239, 239  # the shade of grey for border pixels
   534     opts.label_space = 5     # minimum number of pixels between axis labels
   535 
   536     try: lastDotplot(opts, args)
   537     except KeyboardInterrupt: pass  # avoid silly error message
   538     except Exception, e:
   539         prog = os.path.basename(sys.argv[0])
   540         sys.exit(prog + ": error: " + str(e))