#! /usr/bin/env python

 # Read pair-wise alignments in MAF or LAST tabular format: write an

 # "Oxford grid", a.k.a. dotplot.

 # TODO: Currently, pixels with zero aligned nt-pairs are white, and

 # pixels with one or more aligned nt-pairs are black.  This can look

 # too crowded for large genome alignments.  I tried shading each pixel

 # according to the number of aligned nt-pairs within it, but the

 # result is too faint.  How can this be done better?

 import fnmatch, itertools, optparse, os, re, sys

 # Try to make PIL/PILLOW work:

 try: from PIL import Image, ImageDraw, ImageFont, ImageColor

 except ImportError: import Image, ImageDraw, ImageFont, ImageColor

 def myOpen(fileName):  # faster than fileinput

     if fileName == "-":

         return sys.stdin

     return open(fileName)

 def warn(message):

     prog = os.path.basename(sys.argv[0])

     sys.stderr.write(prog + ": " + message + "\n")

 def croppedBlocks(blocks, range1, range2):

     cropBeg1, cropEnd1 = range1

     cropBeg2, cropEnd2 = range2

     if blocks[0][0] < 0: cropBeg1, cropEnd1 = -cropEnd1, -cropBeg1

     if blocks[0][1] < 0: cropBeg2, cropEnd2 = -cropEnd2, -cropBeg2

     for beg1, beg2, size in blocks:

         b1 = max(cropBeg1, beg1)

         e1 = min(cropEnd1, beg1 + size)

         if b1 >= e1: continue

         offset = beg2 - beg1

         b2 = max(cropBeg2, b1 + offset)

         e2 = min(cropEnd2, e1 + offset)

         if b2 >= e2: continue

         yield b2 - offset, b2, e2 - b2

 def tabBlocks(beg1, beg2, blocks):

     '''Get the gapless blocks of an alignment, from LAST tabular format.'''

     for i in blocks.split(","):

         if ":" in i:

             x, y = i.split(":")

             beg1 += int(x)

             beg2 += int(y)

         else:

             size = int(i)

             yield beg1, beg2, size

             beg1 += size

             beg2 += size

 def mafBlocks(beg1, beg2, seq1, seq2):

     '''Get the gapless blocks of an alignment, from MAF format.'''

     size = 0

     for x, y in itertools.izip(seq1, seq2):

         if x == "-":

             if size:

                 yield beg1, beg2, size

                 beg1 += size

                 beg2 += size

                 size = 0

             beg2 += 1

         elif y == "-":

             if size:

                 yield beg1, beg2, size

                 beg1 += size

                 beg2 += size

                 size = 0

             beg1 += 1

         else:

             size += 1

     if size: yield beg1, beg2, size

 def alignmentInput(lines):

     '''Get alignments and sequence lengths, from MAF or tabular format.'''

     mafCount = 0

     for line in lines:

         w = line.split()

         if line[0].isdigit():  # tabular format

             chr1, beg1, seqlen1 = w[1], int(w[2]), int(w[5])

             if w[4] == "-": beg1 -= seqlen1

             chr2, beg2, seqlen2 = w[6], int(w[7]), int(w[10])

             if w[9] == "-": beg2 -= seqlen2

             blocks = tabBlocks(beg1, beg2, w[11])

             yield chr1, seqlen1, chr2, seqlen2, blocks

         elif line[0] == "s":  # MAF format

             if mafCount == 0:

                 chr1, beg1, seqlen1, seq1 = w[1], int(w[2]), int(w[5]), w[6]

                 if w[4] == "-": beg1 -= seqlen1

                 mafCount = 1

             else:

                 chr2, beg2, seqlen2, seq2 = w[1], int(w[2]), int(w[5]), w[6]

                 if w[4] == "-": beg2 -= seqlen2

                 blocks = mafBlocks(beg1, beg2, seq1, seq2)

                 yield chr1, seqlen1, chr2, seqlen2, blocks

                 mafCount = 0

 def seqRangeFromText(text):

     if ":" in text:

         pattern, interval = text.rsplit(":", 1)

         if "-" in interval:

             beg, end = interval.rsplit("-", 1)

             return pattern, int(beg), int(end)  # beg may be negative

     return text, 0, sys.maxsize

 def rangeFromSeqName(seqRanges, name, seqLen):

     if not seqRanges: return 0, seqLen

     base = name.split(".")[-1]  # allow for names like hg19.chr7

     for pat, beg, end in seqRanges:

         if fnmatch.fnmatchcase(name, pat) or fnmatch.fnmatchcase(base, pat):

             return max(beg, 0), min(end, seqLen)

     return None

 def updateSeqs(isTrim, seqNames, seqLimits, seqName, seqRange, blocks, index):

     if seqName not in seqLimits:

         seqNames.append(seqName)

     if isTrim:

         beg = blocks[0][index]

         end = blocks[-1][index] + blocks[-1][2]

         if beg < 0: beg, end = -end, -beg

         if seqName in seqLimits:

             b, e = seqLimits[seqName]

             seqLimits[seqName] = min(b, beg), max(e, end)

         else:

             seqLimits[seqName] = beg, end

     else:

         seqLimits[seqName] = seqRange

 def readAlignments(fileName, opts):

     '''Get alignments and sequence limits, from MAF or tabular format.'''

     seqRanges1 = map(seqRangeFromText, opts.seq1)

     seqRanges2 = map(seqRangeFromText, opts.seq2)

     alignments = []

     seqNames1 = []

     seqNames2 = []

     seqLimits1 = {}

     seqLimits2 = {}

     lines = myOpen(fileName)

     for seqName1, seqLen1, seqName2, seqLen2, blocks in alignmentInput(lines):

         range1 = rangeFromSeqName(seqRanges1, seqName1, seqLen1)

         if not range1: continue

         range2 = rangeFromSeqName(seqRanges2, seqName2, seqLen2)

         if not range2: continue

         b = list(croppedBlocks(list(blocks), range1, range2))

         if not b: continue

         aln = seqName1, seqName2, b

         alignments.append(aln)

         updateSeqs(opts.trim1, seqNames1, seqLimits1, seqName1, range1, b, 0)

         updateSeqs(opts.trim2, seqNames2, seqLimits2, seqName2, range2, b, 1)

     return alignments, seqNames1, seqNames2, seqLimits1, seqLimits2

 def natural_sort_key(my_string):

     '''Return a sort key for "natural" ordering, e.g. chr9 < chr10.'''

     parts = re.split(r'(\d+)', my_string)

     parts[1::2] = map(int, parts[1::2])

     return parts

 def get_text_sizes(my_strings, font, fontsize, image_mode):

     '''Get widths & heights, in pixels, of some strings.'''

     if fontsize == 0: return [(0, 0) for i in my_strings]

     image_size = 1, 1

     im = Image.new(image_mode, image_size)

     draw = ImageDraw.Draw(im)

     return [draw.textsize(i, font=font) for i in my_strings]

 def sizeText(size):

     suffixes = "bp", "kb", "Mb", "Gb"

     for i, x in enumerate(suffixes):

         j = 10 ** (i * 3)

         if size < j * 10:

             return "%.2g" % (1.0 * size / j) + x

         if size < j * 1000 or i == len(suffixes) - 1:

             return "%.0f" % (1.0 * size / j) + x

 def seqNameAndSizeText(seqName, seqSize):

     return seqName + ": " + sizeText(seqSize)

 def getSeqInfo(sortOpt, seqNames, seqLimits,

                font, fontsize, image_mode, isShowSize):

     '''Return miscellaneous information about the sequences.'''

     if sortOpt == 1:

         seqNames.sort(key=natural_sort_key)

     seqSizes = [seqLimits[i][1] - seqLimits[i][0] for i in seqNames]

     if sortOpt == 2:

         seqRecords = sorted(zip(seqSizes, seqNames), reverse=True)

         seqSizes = [i[0] for i in seqRecords]

         seqNames = [i[1] for i in seqRecords]

     if isShowSize:

         seqLabels = map(seqNameAndSizeText, seqNames, seqSizes)

     else:

         seqLabels = seqNames

     labelSizes = get_text_sizes(seqLabels, font, fontsize, image_mode)

     margin = max(zip(*labelSizes)[1])  # maximum text height

     return seqNames, seqSizes, seqLabels, labelSizes, margin

 def div_ceil(x, y):

     '''Return x / y rounded up.'''

     q, r = divmod(x, y)

     return q + (r != 0)

 def get_bp_per_pix(seq_sizes, pix_tween_seqs, pix_limit):

     '''Get the minimum bp-per-pixel that fits in the size limit.'''

     seq_num = len(seq_sizes)

     seq_pix_limit = pix_limit - pix_tween_seqs * (seq_num - 1)

     if seq_pix_limit < seq_num:

         raise Exception("can't fit the image: too many sequences?")

     negLimit = -seq_pix_limit

     negBpPerPix = sum(seq_sizes) // negLimit

     while True:

         if sum(i // negBpPerPix for i in seq_sizes) >= negLimit:

             return -negBpPerPix

         negBpPerPix -= 1

 def get_seq_starts(seq_pix, pix_tween_seqs, margin):

     '''Get the start pixel for each sequence.'''

     seq_starts = []

     pix_tot = margin - pix_tween_seqs

     for i in seq_pix:

         pix_tot += pix_tween_seqs

         seq_starts.append(pix_tot)

         pix_tot += i

     return seq_starts

 def get_pix_info(seq_sizes, bp_per_pix, pix_tween_seqs, margin):

     '''Return pixel information about the sequences.'''

     seq_pix = [div_ceil(i, bp_per_pix) for i in seq_sizes]

     seq_starts = get_seq_starts(seq_pix, pix_tween_seqs, margin)

     tot_pix = seq_starts[-1] + seq_pix[-1]

     return seq_pix, seq_starts, tot_pix

 def drawLineForward(hits, width, bp_per_pix, beg1, beg2, size):

     while True:

         q1, r1 = divmod(beg1, bp_per_pix)

         q2, r2 = divmod(beg2, bp_per_pix)

         hits[q2 * width + q1] |= 1

         next_pix = min(bp_per_pix - r1, bp_per_pix - r2)

         if next_pix >= size: break

         beg1 += next_pix

         beg2 += next_pix

         size -= next_pix

 def drawLineReverse(hits, width, bp_per_pix, beg1, beg2, size):

     beg2 = -1 - beg2

     while True:

         q1, r1 = divmod(beg1, bp_per_pix)

         q2, r2 = divmod(beg2, bp_per_pix)

         hits[q2 * width + q1] |= 2

         next_pix = min(bp_per_pix - r1, r2 + 1)

         if next_pix >= size: break

         beg1 += next_pix

         beg2 -= next_pix

         size -= next_pix

 def alignmentPixels(width, height, alignments, bp_per_pix, origins1, origins2):

     hits = [0] * (width * height)  # the image data

     for seq1, seq2, blocks in alignments:

         ori1 = origins1[seq1]

         ori2 = origins2[seq2]

         for beg1, beg2, size in blocks:

             if beg1 < 0:

                 beg1 = -(beg1 + size)

                 beg2 = -(beg2 + size)

             if beg2 >= 0:

                 drawLineForward(hits, width, bp_per_pix,

                                 beg1 + ori1, beg2 + ori2, size)

             else:

                 drawLineReverse(hits, width, bp_per_pix,

                                 beg1 + ori1, beg2 - ori2, size)

     return hits

 def expandedSeqDict(seqDict):

     '''Allow lookup by short sequence names, e.g. chr7 as well as hg19.chr7.'''

     newDict = seqDict.copy()

     for name, x in seqDict.items():

         if "." in name:

             base = name.split(".")[-1]

             if base in newDict:  # an ambiguous case was found:

                 return seqDict   # so give up completely

             newDict[base] = x

     return newDict

 def readBed(fileName, seqLimits):

     if not fileName: return

     for line in myOpen(fileName):

         w = line.split()

         if not w: continue

         seqName = w[0]

         if seqName not in seqLimits: continue

         beg = int(w[1])

         end = int(w[2])

         layer = 900

         color = "#ffe4ff"

         if len(w) > 4:

             if w[4] != ".":

                 layer = float(w[4])

             if len(w) > 5:

                 if len(w) > 8 and w[8].count(",") == 2:

                     color = "rgb(" + w[8] + ")"

                 elif w[5] == "+":

                     color = "#fff4f4"

                 elif w[5] == "-":

                     color = "#f4f4ff"

         yield layer, color, seqName, beg, end

 def commaSeparatedInts(text):

     return map(int, text.rstrip(",").split(","))

 def readGenePred(opts, fileName, seqLimits):

     if not fileName: return

     for line in myOpen(fileName):

         fields = line.split()

         if not fields: continue

         if fields[2] not in "+-": fields = fields[1:]

         seqName = fields[1]

         if seqName not in seqLimits: continue

         #strand = fields[2]

         cdsBeg = int(fields[5])

         cdsEnd = int(fields[6])

         exonBegs = commaSeparatedInts(fields[8])

         exonEnds = commaSeparatedInts(fields[9])

         for beg, end in zip(exonBegs, exonEnds):

             yield 300, opts.exon_color, seqName, beg, end

             b = max(beg, cdsBeg)

             e = min(end, cdsEnd)

             if b < e: yield 400, opts.cds_color, seqName, b, e

 def readRmsk(fileName, seqLimits):

     if not fileName: return

     for line in myOpen(fileName):

         fields = line.split()

         if len(fields) == 17:  # rmsk.txt

             seqName = fields[5]

             if seqName not in seqLimits: continue  # do this ASAP for speed

             beg = int(fields[6])

             end = int(fields[7])

             strand = fields[9]

             repeatClass = fields[11]

         elif len(fields) == 15:  # .out

             seqName = fields[4]

             if seqName not in seqLimits: continue

             beg = int(fields[5]) - 1

             end = int(fields[6])

             strand = fields[8]

             repeatClass = fields[10]

         else:

             continue

         if repeatClass in ("Low_complexity", "Simple_repeat"):

             yield 200, "#ffe4ff", seqName, beg, end

         elif strand == "+":

             yield 100, "#fff4f4", seqName, beg, end

         else:

             yield 100, "#f4f4ff", seqName, beg, end

 def isExtraFirstGapField(fields):

     return fields[4].isdigit()

 def readGaps(opts, fileName, seqLimits):

     '''Read locations of unsequenced gaps, from an agp or gap file.'''

     if not fileName: return

     for line in myOpen(fileName):

         w = line.split()

         if not w or w[0][0] == "#": continue

         if isExtraFirstGapField(w): w = w[1:]

         if w[4] not in "NU": continue

         seqName = w[0]

         if seqName not in seqLimits: continue

         end = int(w[2])

         beg = end - int(w[5])  # zero-based coordinate

         if w[7] == "yes":

             yield 3000, opts.bridged_color, seqName, beg, end

         else:

             yield 2000, opts.unbridged_color, seqName, beg, end

 def bedBoxes(beds, seqLimits, origins, margin, edge, isTop, bpPerPix):

     for layer, color, seqName, beg, end in beds:

         cropBeg, cropEnd = seqLimits[seqName]

         beg = max(beg, cropBeg)

         end = min(end, cropEnd)

         if beg >= end: continue

         ori = origins[seqName]

         if layer <= 1000:

             # include partly-covered pixels

             b = (ori + beg) // bpPerPix

             e = div_ceil(ori + end, bpPerPix)

         else:

             # exclude partly-covered pixels

             b = div_ceil(ori + beg, bpPerPix)

             e = (ori + end) // bpPerPix

             if e <= b: continue

         if isTop:

             box = b, margin, e, edge

         else:

             box = margin, b, edge, e

         yield layer, color, box

 def drawAnnotations(im, boxes):

     # xxx use partial transparency for different-color overlaps?

     for layer, color, box in boxes:

         im.paste(color, box)

 def make_label(text, text_size, range_start, range_size):

     '''Return an axis label with endpoint & sort-order information.'''

     text_width  = text_size[0]

     label_start = range_start + (range_size - text_width) // 2

     label_end   = label_start + text_width

     sort_key    = text_width - range_size

     return sort_key, label_start, label_end, text

 def get_nonoverlapping_labels(labels, label_space):

     '''Get a subset of non-overlapping axis labels, greedily.'''

     nonoverlapping_labels = []

     for i in labels:

         if True not in [i[1] < j[2] + label_space and j[1] < i[2] + label_space

                         for j in nonoverlapping_labels]:

             nonoverlapping_labels.append(i)

     return nonoverlapping_labels

 def get_axis_image(seqNames, name_sizes, seq_starts, seq_pix,

                    font, image_mode, opts):

     '''Make an image of axis labels.'''

     min_pos = seq_starts[0]

     max_pos = seq_starts[-1] + seq_pix[-1]

     height = max(zip(*name_sizes)[1])

     labels = map(make_label, seqNames, name_sizes, seq_starts, seq_pix)

     labels = [i for i in labels if i[1] >= min_pos and i[2] <= max_pos]

     labels.sort()

     labels = get_nonoverlapping_labels(labels, opts.label_space)

     image_size = max_pos, height

     im = Image.new(image_mode, image_size, opts.border_color)

     draw = ImageDraw.Draw(im)

     for i in labels:

         position = i[1], 0

         draw.text(position, i[3], font=font, fill=opts.text_color)

     return im

 def seqOrigins(seqNames, seq_starts, seqLimits, bp_per_pix):

     for i, j in zip(seqNames, seq_starts):

         yield i, bp_per_pix * j - seqLimits[i][0]

 def lastDotplot(opts, args):

     if opts.fontfile:  font = ImageFont.truetype(opts.fontfile, opts.fontsize)

     else:              font = ImageFont.load_default()

     image_mode = 'RGB'

     forward_color = ImageColor.getcolor(opts.forwardcolor, image_mode)

     reverse_color = ImageColor.getcolor(opts.reversecolor, image_mode)

     zipped_colors = zip(forward_color, reverse_color)

     overlap_color = tuple([(i + j) // 2 for i, j in zipped_colors])

     warn("reading alignments...")

     alignmentInfo = readAlignments(args[0], opts)

     alignments, seqNames1, seqNames2, seqLimits1, seqLimits2 = alignmentInfo

     warn("done")

     if not alignments: raise Exception("there are no alignments")

     i1 = getSeqInfo(opts.sort1, seqNames1, seqLimits1,

                     font, opts.fontsize, image_mode, opts.lengths1)

     seqNames1, seqSizes1, seqLabels1, labelSizes1, margin1 = i1

     i2 = getSeqInfo(opts.sort2, seqNames2, seqLimits2,

                     font, opts.fontsize, image_mode, opts.lengths2)

     seqNames2, seqSizes2, seqLabels2, labelSizes2, margin2 = i2

     warn("choosing bp per pixel...")

     pix_limit1 = opts.width  - margin1

     pix_limit2 = opts.height - margin2

     bpPerPix1 = get_bp_per_pix(seqSizes1, opts.border_pixels, pix_limit1)

     bpPerPix2 = get_bp_per_pix(seqSizes2, opts.border_pixels, pix_limit2)

     bpPerPix = max(bpPerPix1, bpPerPix2)

     warn("bp per pixel = " + str(bpPerPix))

     seq_pix1, seq_starts1, width  = get_pix_info(seqSizes1, bpPerPix,

                                                  opts.border_pixels, margin1)

     seq_pix2, seq_starts2, height = get_pix_info(seqSizes2, bpPerPix,

                                                  opts.border_pixels, margin2)

     warn("width:  " + str(width))

     warn("height: " + str(height))

     origins1 = dict(seqOrigins(seqNames1, seq_starts1, seqLimits1, bpPerPix))

     origins2 = dict(seqOrigins(seqNames2, seq_starts2, seqLimits2, bpPerPix))

     warn("processing alignments...")

     hits = alignmentPixels(width, height, alignments, bpPerPix,

                            origins1, origins2)

     warn("done")

     image_size = width, height

     im = Image.new(image_mode, image_size, opts.background_color)

     seqLimits1 = expandedSeqDict(seqLimits1)

     seqLimits2 = expandedSeqDict(seqLimits2)

     origins1 = expandedSeqDict(origins1)

     origins2 = expandedSeqDict(origins2)

     beds1 = itertools.chain(readBed(opts.bed1, seqLimits1),

                             readRmsk(opts.rmsk1, seqLimits1),

                             readGenePred(opts, opts.genePred1, seqLimits1),

                             readGaps(opts, opts.gap1, seqLimits1))

     b1 = bedBoxes(beds1, seqLimits1, origins1, margin2, height, True, bpPerPix)

     beds2 = itertools.chain(readBed(opts.bed2, seqLimits2),

                             readRmsk(opts.rmsk2, seqLimits2),

                             readGenePred(opts, opts.genePred2, seqLimits2),

                             readGaps(opts, opts.gap2, seqLimits2))

     b2 = bedBoxes(beds2, seqLimits2, origins2, margin1, width, False, bpPerPix)

     boxes = sorted(itertools.chain(b1, b2))

     drawAnnotations(im, boxes)

     for i in range(height):

         for j in range(width):

             store_value = hits[i * width + j]

             xy = j, i

             if   store_value == 1: im.putpixel(xy, forward_color)

             elif store_value == 2: im.putpixel(xy, reverse_color)

             elif store_value == 3: im.putpixel(xy, overlap_color)

     if opts.fontsize != 0:

         axis1 = get_axis_image(seqLabels1, labelSizes1, seq_starts1, seq_pix1,

                                font, image_mode, opts)

         axis2 = get_axis_image(seqLabels2, labelSizes2, seq_starts2, seq_pix2,

                                font, image_mode, opts)

         axis2 = axis2.transpose(Image.ROTATE_270)  # !!! bug hotspot

         im.paste(axis1, (0, 0))

         im.paste(axis2, (0, 0))

     for i in seq_starts1[1:]:

         box = i - opts.border_pixels, margin2, i, height

         im.paste(opts.border_color, box)

     for i in seq_starts2[1:]:

         box = margin1, i - opts.border_pixels, width, i

         im.paste(opts.border_color, box)

     im.save(args[1])

 if __name__ == "__main__":

     usage = """%prog --help

    or: %prog [options] maf-or-tab-alignments dotplot.png

    or: %prog [options] maf-or-tab-alignments dotplot.gif

    or: ..."""

     description = "Draw a dotplot of pair-wise sequence alignments in MAF or tabular format."

     op = optparse.OptionParser(usage=usage, description=description)

     op.add_option("-1", "--seq1", metavar="PATTERN", action="append",

                   default=[],

                   help="which sequences to show from the 1st genome")

     op.add_option("-2", "--seq2", metavar="PATTERN", action="append",

                   default=[],

                   help="which sequences to show from the 2nd genome")

     # Replace "width" & "height" with a single "length" option?

     op.add_option("-x", "--width", type="int", default=1000,

                   help="maximum width in pixels (default: %default)")

     op.add_option("-y", "--height", type="int", default=1000,

                   help="maximum height in pixels (default: %default)")

     op.add_option("-c", "--forwardcolor", metavar="COLOR", default="red",

                   help="color for forward alignments (default: %default)")

     op.add_option("-r", "--reversecolor", metavar="COLOR", default="blue",

                   help="color for reverse alignments (default: %default)")

     op.add_option("--sort1", type="int", default=1, metavar="N",

                   help="genome1 sequence order: 0=input order, 1=name order, "

                   "2=length order (default=%default)")

     op.add_option("--sort2", type="int", default=1, metavar="N",

                   help="genome2 sequence order: 0=input order, 1=name order, "

                   "2=length order (default=%default)")

     op.add_option("--trim1", action="store_true",

                   help="trim unaligned sequence flanks from the 1st genome")

     op.add_option("--trim2", action="store_true",

                   help="trim unaligned sequence flanks from the 2nd genome")

     op.add_option("--border-pixels", metavar="INT", type="int", default=1,

                   help="number of pixels between sequences (default=%default)")

     op.add_option("--border-color", metavar="COLOR", default="#dcdcdc",

                   help="color for pixels between sequences (default=%default)")

     # xxx --margin-color?

     og = optparse.OptionGroup(op, "Text options")

     og.add_option("-f", "--fontfile", metavar="FILE",

                   help="TrueType or OpenType font file")

     og.add_option("-s", "--fontsize", metavar="SIZE", type="int", default=11,

                   help="TrueType or OpenType font size (default: %default)")

     og.add_option("--lengths1", action="store_true",

                   help="show sequence lengths for the 1st (horizontal) genome")

     og.add_option("--lengths2", action="store_true",

                   help="show sequence lengths for the 2nd (vertical) genome")

     op.add_option_group(og)

     og = optparse.OptionGroup(op, "Annotation options")

     og.add_option("--bed1", metavar="FILE",

                   help="read genome1 annotations from BED file")

     og.add_option("--bed2", metavar="FILE",

                   help="read genome2 annotations from BED file")

     og.add_option("--rmsk1", metavar="FILE", help="read genome1 repeats from "

                   "RepeatMasker .out or rmsk.txt file")

     og.add_option("--rmsk2", metavar="FILE", help="read genome2 repeats from "

                   "RepeatMasker .out or rmsk.txt file")

     op.add_option_group(og)

     og = optparse.OptionGroup(op, "Gene options")

     og.add_option("--genePred1", metavar="FILE",

                   help="read genome1 genes from genePred file")

     og.add_option("--genePred2", metavar="FILE",

                   help="read genome2 genes from genePred file")

     og.add_option("--exon-color", metavar="COLOR", default="#dfd",

                   help="color for exons (default=%default)")

     og.add_option("--cds-color", metavar="COLOR", default="#bdb",

                   help="color for protein-coding regions (default=%default)")

     op.add_option_group(og)

     og = optparse.OptionGroup(op, "Unsequenced gap options")

     og.add_option("--gap1", metavar="FILE",

                   help="read genome1 unsequenced gaps from agp or gap file")

     og.add_option("--gap2", metavar="FILE",

                   help="read genome2 unsequenced gaps from agp or gap file")

     og.add_option("--bridged-color", metavar="COLOR", default="yellow",

                   help="color for bridged gaps (default: %default)")

     og.add_option("--unbridged-color", metavar="COLOR", default="pink",

                   help="color for unbridged gaps (default: %default)")

     op.add_option_group(og)

     (opts, args) = op.parse_args()

     if len(args) != 2: op.error("2 arguments needed")

     opts.text_color = "black"

     opts.background_color = "white"

     opts.label_space = 5     # minimum number of pixels between axis labels

     try: lastDotplot(opts, args)

     except KeyboardInterrupt: pass  # avoid silly error message

     except Exception, e:

         prog = os.path.basename(sys.argv[0])

         sys.exit(prog + ": error: " + str(e))