scripts/last-dotplot
author Martin C. Frith
Thu Jul 30 21:47:07 2020 +0900 (21 months ago)
changeset 1070 6cf9358f80da
parent 1069 da8b081ec496
child 1071 c5d3cf8c1058
permissions -rwxr-xr-x
last-dotplot: refactor
     1 #! /usr/bin/env python
     2 # Author: Martin C. Frith 2008
     3 # SPDX-License-Identifier: GPL-3.0-or-later
     4 
     5 # Read pair-wise alignments in MAF or LAST tabular format: write an
     6 # "Oxford grid", a.k.a. dotplot.
     7 
     8 # TODO: Currently, pixels with zero aligned nt-pairs are white, and
     9 # pixels with one or more aligned nt-pairs are black.  This can look
    10 # too crowded for large genome alignments.  I tried shading each pixel
    11 # according to the number of aligned nt-pairs within it, but the
    12 # result is too faint.  How can this be done better?
    13 
    14 import collections
    15 import functools
    16 import gzip
    17 from fnmatch import fnmatchcase
    18 import logging
    19 from operator import itemgetter
    20 import subprocess
    21 import itertools, optparse, os, re, sys
    22 
    23 # Try to make PIL/PILLOW work:
    24 try:
    25     from PIL import Image, ImageDraw, ImageFont, ImageColor
    26 except ImportError:
    27     import Image, ImageDraw, ImageFont, ImageColor
    28 
    29 try:
    30     from future_builtins import zip
    31 except ImportError:
    32     pass
    33 
    34 def myOpen(fileName):  # faster than fileinput
    35     if fileName is None:
    36         return []
    37     if fileName == "-":
    38         return sys.stdin
    39     if fileName.endswith(".gz"):
    40         return gzip.open(fileName, "rt")  # xxx dubious for Python2
    41     return open(fileName)
    42 
    43 def groupByFirstItem(things):
    44     for k, v in itertools.groupby(things, itemgetter(0)):
    45         yield k, [i[1:] for i in v]
    46 
    47 def croppedBlocks(blocks, ranges1, ranges2):
    48     headBeg1, headBeg2, headSize = blocks[0]
    49     for r1 in ranges1:
    50         for r2 in ranges2:
    51             cropBeg1, cropEnd1 = r1
    52             if headBeg1 < 0:
    53                 cropBeg1, cropEnd1 = -cropEnd1, -cropBeg1
    54             cropBeg2, cropEnd2 = r2
    55             if headBeg2 < 0:
    56                 cropBeg2, cropEnd2 = -cropEnd2, -cropBeg2
    57             for beg1, beg2, size in blocks:
    58                 b1 = max(cropBeg1, beg1)
    59                 e1 = min(cropEnd1, beg1 + size)
    60                 if b1 >= e1: continue
    61                 offset = beg2 - beg1
    62                 b2 = max(cropBeg2, b1 + offset)
    63                 e2 = min(cropEnd2, e1 + offset)
    64                 if b2 >= e2: continue
    65                 yield b2 - offset, b2, e2 - b2
    66 
    67 def tabBlocks(beg1, beg2, blocks):
    68     '''Get the gapless blocks of an alignment, from LAST tabular format.'''
    69     for i in blocks.split(","):
    70         if ":" in i:
    71             x, y = i.split(":")
    72             beg1 += int(x)
    73             beg2 += int(y)
    74         else:
    75             size = int(i)
    76             yield beg1, beg2, size
    77             beg1 += size
    78             beg2 += size
    79 
    80 def mafBlocks(beg1, beg2, seq1, seq2):
    81     '''Get the gapless blocks of an alignment, from MAF format.'''
    82     size = 0
    83     for x, y in zip(seq1, seq2):
    84         if x == "-":
    85             if size:
    86                 yield beg1, beg2, size
    87                 beg1 += size
    88                 beg2 += size
    89                 size = 0
    90             beg2 += 1
    91         elif y == "-":
    92             if size:
    93                 yield beg1, beg2, size
    94                 beg1 += size
    95                 beg2 += size
    96                 size = 0
    97             beg1 += 1
    98         else:
    99             size += 1
   100     if size: yield beg1, beg2, size
   101 
   102 def alignmentFromSegment(qrySeqName, qrySeqLen, segment):
   103     refSeqLen = sys.maxsize  # XXX
   104     refSeqName, refSeqBeg, qrySeqBeg, size = segment
   105     block = refSeqBeg, qrySeqBeg, size
   106     return refSeqName, refSeqLen, qrySeqName, qrySeqLen, [block]
   107 
   108 def alignmentInput(lines):
   109     '''Get alignments and sequence lengths, from MAF or tabular format.'''
   110     mafCount = 0
   111     qrySeqName = ""
   112     segments = []
   113     for line in lines:
   114         w = line.split()
   115         if line[0] == "#":
   116             pass
   117         elif len(w) == 1:
   118             for i in segments:
   119                 yield alignmentFromSegment(qrySeqName, qrySeqLen, i)
   120             qrySeqName = w[0]
   121             qrySeqLen = 0
   122             segments = []
   123         elif len(w) == 2 and qrySeqName and w[1].isdigit():
   124             qrySeqLen += int(w[1])
   125         elif len(w) == 4 and qrySeqName and w[1].isdigit() and w[3].isdigit():
   126             refSeqName, refSeqBeg, refSeqEnd = w[0], int(w[1]), int(w[3])
   127             size = abs(refSeqEnd - refSeqBeg)
   128             if refSeqBeg > refSeqEnd:
   129                 refSeqBeg = -refSeqBeg
   130             segments.append((refSeqName, refSeqBeg, qrySeqLen, size))
   131             qrySeqLen += size
   132         elif line[0].isdigit():  # tabular format
   133             chr1, beg1, seqlen1 = w[1], int(w[2]), int(w[5])
   134             if w[4] == "-": beg1 -= seqlen1
   135             chr2, beg2, seqlen2 = w[6], int(w[7]), int(w[10])
   136             if w[9] == "-": beg2 -= seqlen2
   137             blocks = tabBlocks(beg1, beg2, w[11])
   138             yield chr1, seqlen1, chr2, seqlen2, blocks
   139         elif line[0] == "s":  # MAF format
   140             if mafCount == 0:
   141                 chr1, beg1, seqlen1, seq1 = w[1], int(w[2]), int(w[5]), w[6]
   142                 if w[4] == "-": beg1 -= seqlen1
   143                 mafCount = 1
   144             else:
   145                 chr2, beg2, seqlen2, seq2 = w[1], int(w[2]), int(w[5]), w[6]
   146                 if w[4] == "-": beg2 -= seqlen2
   147                 blocks = mafBlocks(beg1, beg2, seq1, seq2)
   148                 yield chr1, seqlen1, chr2, seqlen2, blocks
   149                 mafCount = 0
   150     for i in segments:
   151         yield alignmentFromSegment(qrySeqName, qrySeqLen, i)
   152 
   153 def seqRequestFromText(text):
   154     if ":" in text:
   155         pattern, interval = text.rsplit(":", 1)
   156         if "-" in interval:
   157             beg, end = interval.rsplit("-", 1)
   158             return pattern, int(beg), int(end)  # beg may be negative
   159     return text, 0, sys.maxsize
   160 
   161 def rangesFromSeqName(seqRequests, name, seqLen):
   162     if seqRequests:
   163         base = name.split(".")[-1]  # allow for names like hg19.chr7
   164         for pat, beg, end in seqRequests:
   165             if fnmatchcase(name, pat) or fnmatchcase(base, pat):
   166                 yield max(beg, 0), min(end, seqLen)
   167     else:
   168         yield 0, seqLen
   169 
   170 def updateSeqs(coverDict, seqRanges, seqName, ranges, coveredRange):
   171     beg, end = coveredRange
   172     if beg < 0:
   173         coveredRange = -end, -beg
   174     if seqName in coverDict:
   175         coverDict[seqName].append(coveredRange)
   176     else:
   177         coverDict[seqName] = [coveredRange]
   178         for beg, end in ranges:
   179             r = seqName, beg, end
   180             seqRanges.append(r)
   181 
   182 def readAlignments(fileName, opts):
   183     '''Get alignments and sequence limits, from MAF or tabular format.'''
   184     seqRequests1 = [seqRequestFromText(i) for i in opts.seq1]
   185     seqRequests2 = [seqRequestFromText(i) for i in opts.seq2]
   186 
   187     alignments = []
   188     seqRanges1 = []
   189     seqRanges2 = []
   190     coverDict1 = {}
   191     coverDict2 = {}
   192     lines = myOpen(fileName)
   193     for seqName1, seqLen1, seqName2, seqLen2, blocks in alignmentInput(lines):
   194         ranges1 = sorted(rangesFromSeqName(seqRequests1, seqName1, seqLen1))
   195         if not ranges1: continue
   196         ranges2 = sorted(rangesFromSeqName(seqRequests2, seqName2, seqLen2))
   197         if not ranges2: continue
   198         b = list(croppedBlocks(list(blocks), ranges1, ranges2))
   199         if not b: continue
   200         aln = seqName1, seqName2, b
   201         alignments.append(aln)
   202         coveredRange1 = b[0][0], b[-1][0] + b[-1][2]
   203         updateSeqs(coverDict1, seqRanges1, seqName1, ranges1, coveredRange1)
   204         coveredRange2 = b[0][1], b[-1][1] + b[-1][2]
   205         updateSeqs(coverDict2, seqRanges2, seqName2, ranges2, coveredRange2)
   206     return alignments, seqRanges1, coverDict1, seqRanges2, coverDict2
   207 
   208 def nameAndRangesFromDict(cropDict, seqName):
   209     if seqName in cropDict:
   210         return seqName, cropDict[seqName]
   211     n = seqName.split(".")[-1]
   212     if n in cropDict:
   213         return n, cropDict[n]
   214     return seqName, []
   215 
   216 def rangesForSecondaryAlignments(primaryRanges, seqLen):
   217     if primaryRanges:
   218         return primaryRanges
   219     return [(0, seqLen)]
   220 
   221 def readSecondaryAlignments(opts, cropRanges1, cropRanges2):
   222     cropDict1 = dict(groupByFirstItem(cropRanges1))
   223     cropDict2 = dict(groupByFirstItem(cropRanges2))
   224 
   225     alignments = []
   226     seqRanges1 = []
   227     seqRanges2 = []
   228     coverDict1 = {}
   229     coverDict2 = {}
   230     lines = myOpen(opts.alignments)
   231     for seqName1, seqLen1, seqName2, seqLen2, blocks in alignmentInput(lines):
   232         seqName1, ranges1 = nameAndRangesFromDict(cropDict1, seqName1)
   233         seqName2, ranges2 = nameAndRangesFromDict(cropDict2, seqName2)
   234         if not ranges1 and not ranges2:
   235             continue
   236         r1 = rangesForSecondaryAlignments(ranges1, seqLen1)
   237         r2 = rangesForSecondaryAlignments(ranges2, seqLen2)
   238         b = list(croppedBlocks(list(blocks), r1, r2))
   239         if not b: continue
   240         aln = seqName1, seqName2, b
   241         alignments.append(aln)
   242         if not ranges1:
   243             coveredRange1 = b[0][0], b[-1][0] + b[-1][2]
   244             updateSeqs(coverDict1, seqRanges1, seqName1, r1, coveredRange1)
   245         if not ranges2:
   246             coveredRange2 = b[0][1], b[-1][1] + b[-1][2]
   247             updateSeqs(coverDict2, seqRanges2, seqName2, r2, coveredRange2)
   248     return alignments, seqRanges1, coverDict1, seqRanges2, coverDict2
   249 
   250 def twoValuesFromOption(text, separator):
   251     if separator in text:
   252         return text.split(separator)
   253     return text, text
   254 
   255 def mergedRanges(ranges):
   256     oldBeg, maxEnd = ranges[0]
   257     for beg, end in ranges:
   258         if beg > maxEnd:
   259             yield oldBeg, maxEnd
   260             oldBeg = beg
   261             maxEnd = end
   262         elif end > maxEnd:
   263             maxEnd = end
   264     yield oldBeg, maxEnd
   265 
   266 def mergedRangesPerSeq(coverDict):
   267     for k, v in coverDict.items():
   268         v.sort()
   269         yield k, list(mergedRanges(v))
   270 
   271 def coveredLength(mergedCoverDict):
   272     return sum(sum(e - b for b, e in v) for v in mergedCoverDict.values())
   273 
   274 def trimmed(seqRanges, coverDict, minAlignedBases, maxGapFrac, endPad, midPad):
   275     maxEndGapFrac, maxMidGapFrac = twoValuesFromOption(maxGapFrac, ",")
   276     maxEndGap = max(float(maxEndGapFrac) * minAlignedBases, endPad * 1.0)
   277     maxMidGap = max(float(maxMidGapFrac) * minAlignedBases, midPad * 2.0)
   278 
   279     for seqName, rangeBeg, rangeEnd in seqRanges:
   280         seqBlocks = coverDict[seqName]
   281         blocks = [i for i in seqBlocks if i[0] < rangeEnd and i[1] > rangeBeg]
   282         if blocks[0][0] - rangeBeg > maxEndGap:
   283             rangeBeg = blocks[0][0] - endPad
   284         for j, y in enumerate(blocks):
   285             if j:
   286                 x = blocks[j - 1]
   287                 if y[0] - x[1] > maxMidGap:
   288                     yield seqName, rangeBeg, x[1] + midPad
   289                     rangeBeg = y[0] - midPad
   290         if rangeEnd - blocks[-1][1] > maxEndGap:
   291             rangeEnd = blocks[-1][1] + endPad
   292         yield seqName, rangeBeg, rangeEnd
   293 
   294 def rangesWithStrandInfo(seqRanges, strandOpt, alignments, seqIndex):
   295     if strandOpt == "1":
   296         forwardMinusReverse = collections.defaultdict(int)
   297         for i in alignments:
   298             blocks = i[2]
   299             beg1, beg2, size = blocks[0]
   300             numOfAlignedLetterPairs = sum(i[2] for i in blocks)
   301             if (beg1 < 0) != (beg2 < 0):  # opposite-strand alignment
   302                 numOfAlignedLetterPairs *= -1
   303             forwardMinusReverse[i[seqIndex]] += numOfAlignedLetterPairs
   304     strandNum = 0
   305     for seqName, beg, end in seqRanges:
   306         if strandOpt == "1":
   307             strandNum = 1 if forwardMinusReverse[seqName] >= 0 else 2
   308         yield seqName, beg, end, strandNum
   309 
   310 def natural_sort_key(my_string):
   311     '''Return a sort key for "natural" ordering, e.g. chr9 < chr10.'''
   312     parts = re.split(r'(\d+)', my_string)
   313     parts[1::2] = map(int, parts[1::2])
   314     return parts
   315 
   316 def nameKey(oneSeqRanges):
   317     return natural_sort_key(oneSeqRanges[0][0])
   318 
   319 def sizeKey(oneSeqRanges):
   320     return sum(b - e for n, b, e, s in oneSeqRanges), nameKey(oneSeqRanges)
   321 
   322 def alignmentKey(seqNamesToLists, oneSeqRanges):
   323     seqName = oneSeqRanges[0][0]
   324     alignmentsOfThisSequence = seqNamesToLists[seqName]
   325     numOfAlignedLetterPairs = sum(i[3] for i in alignmentsOfThisSequence)
   326     toMiddle = numOfAlignedLetterPairs // 2
   327     for i in alignmentsOfThisSequence:
   328         toMiddle -= i[3]
   329         if toMiddle < 0:
   330             return i[1:3]  # sequence-rank and "position" of this alignment
   331 
   332 def rankAndFlipPerSeq(seqRanges):
   333     rangesGroupedBySeqName = itertools.groupby(seqRanges, itemgetter(0))
   334     for rank, group in enumerate(rangesGroupedBySeqName):
   335         seqName, ranges = group
   336         strandNum = next(ranges)[3]
   337         flip = 1 if strandNum < 2 else -1
   338         yield seqName, (rank, flip)
   339 
   340 def alignmentSortData(alignments, seqIndex, otherNamesToRanksAndFlips):
   341     otherIndex = 1 - seqIndex
   342     for i in alignments:
   343         blocks = i[2]
   344         otherRank, otherFlip = otherNamesToRanksAndFlips[i[otherIndex]]
   345         otherPos = otherFlip * abs(blocks[0][otherIndex] +
   346                                    blocks[-1][otherIndex] + blocks[-1][2])
   347         numOfAlignedLetterPairs = sum(i[2] for i in blocks)
   348         yield i[seqIndex], otherRank, otherPos, numOfAlignedLetterPairs
   349 
   350 def mySortedRanges(seqRanges, sortOpt, seqIndex, alignments, otherRanges):
   351     rangesGroupedBySeqName = itertools.groupby(seqRanges, itemgetter(0))
   352     g = [list(ranges) for seqName, ranges in rangesGroupedBySeqName]
   353     for i in g:
   354         if i[0][3] > 1:
   355             i.reverse()
   356     if sortOpt == "1":
   357         g.sort(key=nameKey)
   358     if sortOpt == "2":
   359         g.sort(key=sizeKey)
   360     if sortOpt == "3":
   361         otherNamesToRanksAndFlips = dict(rankAndFlipPerSeq(otherRanges))
   362         alns = sorted(alignmentSortData(alignments, seqIndex,
   363                                         otherNamesToRanksAndFlips))
   364         alnsGroupedBySeqName = itertools.groupby(alns, itemgetter(0))
   365         seqNamesToLists = dict((k, list(v)) for k, v in alnsGroupedBySeqName)
   366         g.sort(key=functools.partial(alignmentKey, seqNamesToLists))
   367     return [j for i in g for j in i]
   368 
   369 def allSortedRanges(opts, alignments, alignmentsB,
   370                     seqRanges1, seqRangesB1, seqRanges2, seqRangesB2):
   371     o1, oB1 = twoValuesFromOption(opts.strands1, ":")
   372     o2, oB2 = twoValuesFromOption(opts.strands2, ":")
   373     if o1 == "1" and o2 == "1":
   374         raise Exception("the strand options have circular dependency")
   375     seqRanges1 = list(rangesWithStrandInfo(seqRanges1, o1, alignments, 0))
   376     seqRanges2 = list(rangesWithStrandInfo(seqRanges2, o2, alignments, 1))
   377     seqRangesB1 = list(rangesWithStrandInfo(seqRangesB1, oB1, alignmentsB, 0))
   378     seqRangesB2 = list(rangesWithStrandInfo(seqRangesB2, oB2, alignmentsB, 1))
   379 
   380     o1, oB1 = twoValuesFromOption(opts.sort1, ":")
   381     o2, oB2 = twoValuesFromOption(opts.sort2, ":")
   382     if o1 == "3" and o2 == "3":
   383         raise Exception("the sort options have circular dependency")
   384     if o1 != "3":
   385         s1 = mySortedRanges(seqRanges1, o1, None, None, None)
   386     if o2 != "3":
   387         s2 = mySortedRanges(seqRanges2, o2, None, None, None)
   388     if o1 == "3":
   389         s1 = mySortedRanges(seqRanges1, o1, 0, alignments, s2)
   390     if o2 == "3":
   391         s2 = mySortedRanges(seqRanges2, o2, 1, alignments, s1)
   392     t1 = mySortedRanges(seqRangesB1, oB1, 0, alignmentsB, s2)
   393     t2 = mySortedRanges(seqRangesB2, oB2, 1, alignmentsB, s1)
   394     return s1 + t1, s2 + t2
   395 
   396 def prettyNum(n):
   397     t = str(n)
   398     groups = []
   399     while t:
   400         groups.append(t[-3:])
   401         t = t[:-3]
   402     return ",".join(reversed(groups))
   403 
   404 def sizeText(size):
   405     suffixes = "bp", "kb", "Mb", "Gb"
   406     for i, x in enumerate(suffixes):
   407         j = 10 ** (i * 3)
   408         if size < j * 10:
   409             return "%.2g" % (1.0 * size / j) + x
   410         if size < j * 1000 or i == len(suffixes) - 1:
   411             return "%.0f" % (1.0 * size / j) + x
   412 
   413 def labelText(seqRange, labelOpt):
   414     seqName, beg, end, strandNum = seqRange
   415     if labelOpt == 1:
   416         return seqName + ": " + sizeText(end - beg)
   417     if labelOpt == 2:
   418         return seqName + ":" + prettyNum(beg) + ": " + sizeText(end - beg)
   419     if labelOpt == 3:
   420         return seqName + ":" + prettyNum(beg) + "-" + prettyNum(end)
   421     return seqName
   422 
   423 def rangeLabels(seqRanges, labelOpt, font, textDraw, textRot):
   424     x = y = 0
   425     for r in seqRanges:
   426         text = labelText(r, labelOpt)
   427         if textDraw is not None:
   428             x, y = textDraw.textsize(text, font=font)
   429             if textRot:
   430                 x, y = y, x
   431         yield text, x, y, r[3]
   432 
   433 def dataFromRanges(sortedRanges, font, textDraw, labelOpt, textRot):
   434     for seqName, rangeBeg, rangeEnd, strandNum in sortedRanges:
   435         out = [seqName, str(rangeBeg), str(rangeEnd)]
   436         if strandNum > 0:
   437             out.append(".+-"[strandNum])
   438         logging.info("\t".join(out))
   439     logging.info("")
   440     rangeSizes = [e - b for n, b, e, s in sortedRanges]
   441     labs = list(rangeLabels(sortedRanges, labelOpt, font, textDraw, textRot))
   442     margin = max(i[2] for i in labs)
   443     # xxx the margin may be too big, because some labels may get omitted
   444     return rangeSizes, labs, margin
   445 
   446 def div_ceil(x, y):
   447     '''Return x / y rounded up.'''
   448     q, r = divmod(x, y)
   449     return q + (r != 0)
   450 
   451 def get_bp_per_pix(rangeSizes, pixTweenRanges, maxPixels):
   452     '''Get the minimum bp-per-pixel that fits in the size limit.'''
   453     logging.info("choosing bp per pixel...")
   454     numOfRanges = len(rangeSizes)
   455     maxPixelsInRanges = maxPixels - pixTweenRanges * (numOfRanges - 1)
   456     if maxPixelsInRanges < numOfRanges:
   457         raise Exception("can't fit the image: too many sequences?")
   458     negLimit = -maxPixelsInRanges
   459     negBpPerPix = sum(rangeSizes) // negLimit
   460     while True:
   461         if sum(i // negBpPerPix for i in rangeSizes) >= negLimit:
   462             return -negBpPerPix
   463         negBpPerPix -= 1
   464 
   465 def getRangePixBegs(rangePixLens, pixTweenRanges, margin):
   466     '''Get the start pixel for each range.'''
   467     rangePixBegs = []
   468     pix_tot = margin - pixTweenRanges
   469     for i in rangePixLens:
   470         pix_tot += pixTweenRanges
   471         rangePixBegs.append(pix_tot)
   472         pix_tot += i
   473     return rangePixBegs
   474 
   475 def pixelData(rangeSizes, bp_per_pix, pixTweenRanges, margin):
   476     '''Return pixel information about the ranges.'''
   477     rangePixLens = [div_ceil(i, bp_per_pix) for i in rangeSizes]
   478     rangePixBegs = getRangePixBegs(rangePixLens, pixTweenRanges, margin)
   479     tot_pix = rangePixBegs[-1] + rangePixLens[-1]
   480     return rangePixBegs, rangePixLens, tot_pix
   481 
   482 def drawLineForward(hits, width, bp_per_pix, beg1, beg2, size):
   483     while True:
   484         q1, r1 = divmod(beg1, bp_per_pix)
   485         q2, r2 = divmod(beg2, bp_per_pix)
   486         hits[q2 * width + q1] |= 1
   487         next_pix = min(bp_per_pix - r1, bp_per_pix - r2)
   488         if next_pix >= size: break
   489         beg1 += next_pix
   490         beg2 += next_pix
   491         size -= next_pix
   492 
   493 def drawLineReverse(hits, width, bp_per_pix, beg1, beg2, size):
   494     while True:
   495         q1, r1 = divmod(beg1, bp_per_pix)
   496         q2, r2 = divmod(beg2, bp_per_pix)
   497         hits[q2 * width + q1] |= 2
   498         next_pix = min(bp_per_pix - r1, r2 + 1)
   499         if next_pix >= size: break
   500         beg1 += next_pix
   501         beg2 -= next_pix
   502         size -= next_pix
   503 
   504 def strandAndOrigin(ranges, beg, size):
   505     isReverseStrand = (beg < 0)
   506     if isReverseStrand:
   507         beg = -(beg + size)
   508     for rangeBeg, rangeEnd, isReverseRange, origin in ranges:
   509         if rangeEnd > beg:  # assumes the ranges are sorted
   510             return (isReverseStrand != isReverseRange), origin
   511 
   512 def alignmentPixels(width, height, alignments, bp_per_pix,
   513                     rangeDict1, rangeDict2):
   514     hits = [0] * (width * height)  # the image data
   515     for seq1, seq2, blocks in alignments:
   516         beg1, beg2, size = blocks[0]
   517         isReverse1, ori1 = strandAndOrigin(rangeDict1[seq1], beg1, size)
   518         isReverse2, ori2 = strandAndOrigin(rangeDict2[seq2], beg2, size)
   519         for beg1, beg2, size in blocks:
   520             if isReverse1:
   521                 beg1 = -(beg1 + size)
   522                 beg2 = -(beg2 + size)
   523             if isReverse1 == isReverse2:
   524                 drawLineForward(hits, width, bp_per_pix,
   525                                 ori1 + beg1, ori2 + beg2, size)
   526             else:
   527                 drawLineReverse(hits, width, bp_per_pix,
   528                                 ori1 + beg1, ori2 - beg2 - 1, size)
   529     return hits
   530 
   531 def orientedBlocks(alignments, seqIndex):
   532     otherIndex = 1 - seqIndex
   533     for a in alignments:
   534         seq1, seq2, blocks = a
   535         for b in blocks:
   536             beg1, beg2, size = b
   537             if b[seqIndex] < 0:
   538                 b = -(beg1 + size), -(beg2 + size), size
   539             yield a[seqIndex], b[seqIndex], a[otherIndex], b[otherIndex], size
   540 
   541 def drawJoins(im, alignments, bpPerPix, seqIndex, rangeDict1, rangeDict2):
   542     blocks = orientedBlocks(alignments, seqIndex)
   543     oldSeq1 = ""
   544     for seq1, beg1, seq2, beg2, size in sorted(blocks):
   545         isReverse1, ori1 = strandAndOrigin(rangeDict1[seq1], beg1, size)
   546         isReverse2, ori2 = strandAndOrigin(rangeDict2[seq2], beg2, size)
   547         end1 = beg1 + size - 1
   548         end2 = beg2 + size - 1
   549         if isReverse1:
   550             beg1 = -(beg1 + 1)
   551             end1 = -(end1 + 1)
   552         if isReverse2:
   553             beg2 = -(beg2 + 1)
   554             end2 = -(end2 + 1)
   555         newPix1 = (ori1 + beg1) // bpPerPix
   556         newPix2 = (ori2 + beg2) // bpPerPix
   557         if seq1 == oldSeq1:
   558             lowerPix2 = min(oldPix2, newPix2)
   559             upperPix2 = max(oldPix2, newPix2)
   560             midPix1 = (oldPix1 + newPix1) // 2
   561             if isReverse1:
   562                 midPix1 = (oldPix1 + newPix1 + 1) // 2
   563                 oldPix1, newPix1 = newPix1, oldPix1
   564             if upperPix2 - lowerPix2 > 1 and oldPix1 <= newPix1 <= oldPix1 + 1:
   565                 if seqIndex == 0:
   566                     box = midPix1, lowerPix2, midPix1 + 1, upperPix2 + 1
   567                 else:
   568                     box = lowerPix2, midPix1, upperPix2 + 1, midPix1 + 1
   569                 im.paste("lightgray", box)
   570         oldPix1 = (ori1 + end1) // bpPerPix
   571         oldPix2 = (ori2 + end2) // bpPerPix
   572         oldSeq1 = seq1
   573 
   574 def expandedSeqDict(seqDict):
   575     '''Allow lookup by short sequence names, e.g. chr7 as well as hg19.chr7.'''
   576     newDict = seqDict.copy()
   577     for name, x in seqDict.items():
   578         if "." in name:
   579             base = name.split(".")[-1]
   580             if base in newDict:  # an ambiguous case was found:
   581                 return seqDict   # so give up completely
   582             newDict[base] = x
   583     return newDict
   584 
   585 def readBed(fileName, rangeDict):
   586     for line in myOpen(fileName):
   587         w = line.split()
   588         if not w: continue
   589         seqName = w[0]
   590         if seqName not in rangeDict: continue
   591         beg = int(w[1])
   592         end = int(w[2])
   593         layer = 900
   594         color = "#fbf"
   595         if len(w) > 4:
   596             if w[4] != ".":
   597                 layer = float(w[4])
   598             if len(w) > 5:
   599                 if len(w) > 8 and w[8].count(",") == 2:
   600                     color = "rgb(" + w[8] + ")"
   601                 else:
   602                     strand = w[5]
   603                     isRev = rangeDict[seqName][0][2]
   604                     if strand == "+" and not isRev or strand == "-" and isRev:
   605                         color = "#ffe8e8"
   606                     if strand == "-" and not isRev or strand == "+" and isRev:
   607                         color = "#e8e8ff"
   608         yield layer, color, seqName, beg, end
   609 
   610 def commaSeparatedInts(text):
   611     return map(int, text.rstrip(",").split(","))
   612 
   613 def readGenePred(opts, fileName, rangeDict):
   614     for line in myOpen(fileName):
   615         fields = line.split()
   616         if not fields: continue
   617         if fields[2] not in "+-":
   618             fields = fields[1:]
   619         seqName = fields[1]
   620         if seqName not in rangeDict: continue
   621         #strand = fields[2]
   622         cdsBeg = int(fields[5])
   623         cdsEnd = int(fields[6])
   624         exonBegs = commaSeparatedInts(fields[8])
   625         exonEnds = commaSeparatedInts(fields[9])
   626         for beg, end in zip(exonBegs, exonEnds):
   627             yield 300, opts.exon_color, seqName, beg, end
   628             b = max(beg, cdsBeg)
   629             e = min(end, cdsEnd)
   630             if b < e: yield 400, opts.cds_color, seqName, b, e
   631 
   632 def readRmsk(fileName, rangeDict):
   633     for line in myOpen(fileName):
   634         fields = line.split()
   635         if len(fields) == 17:  # rmsk.txt
   636             seqName = fields[5]
   637             if seqName not in rangeDict: continue  # do this ASAP for speed
   638             beg = int(fields[6])
   639             end = int(fields[7])
   640             strand = fields[9]
   641             repeatClass = fields[11]
   642         elif len(fields) == 15:  # .out
   643             seqName = fields[4]
   644             if seqName not in rangeDict: continue
   645             beg = int(fields[5]) - 1
   646             end = int(fields[6])
   647             strand = fields[8]
   648             repeatClass = fields[10].split("/")[0]
   649         else:
   650             continue
   651         if repeatClass in ("Low_complexity", "Simple_repeat", "Satellite"):
   652             yield 200, "#fbf", seqName, beg, end
   653         elif (strand == "+") != rangeDict[seqName][0][2]:
   654             yield 100, "#ffe8e8", seqName, beg, end
   655         else:
   656             yield 100, "#e8e8ff", seqName, beg, end
   657 
   658 def isExtraFirstGapField(fields):
   659     return fields[4].isdigit()
   660 
   661 def readGaps(opts, fileName, rangeDict):
   662     '''Read locations of unsequenced gaps, from an agp or gap file.'''
   663     for line in myOpen(fileName):
   664         w = line.split()
   665         if not w or w[0][0] == "#": continue
   666         if isExtraFirstGapField(w): w = w[1:]
   667         if w[4] not in "NU": continue
   668         seqName = w[0]
   669         if seqName not in rangeDict: continue
   670         end = int(w[2])
   671         beg = end - int(w[5])  # zero-based coordinate
   672         if w[7] == "yes":
   673             yield 3000, opts.bridged_color, seqName, beg, end
   674         else:
   675             yield 2000, opts.unbridged_color, seqName, beg, end
   676 
   677 def bedBoxes(beds, rangeDict, margin, edge, isTop, bpPerPix):
   678     for layer, color, seqName, bedBeg, bedEnd in beds:
   679         for rangeBeg, rangeEnd, isReverseRange, origin in rangeDict[seqName]:
   680             beg = max(bedBeg, rangeBeg)
   681             end = min(bedEnd, rangeEnd)
   682             if beg >= end: continue
   683             if isReverseRange:
   684                 beg, end = -end, -beg
   685             if layer <= 1000:
   686                 # include partly-covered pixels
   687                 b = (origin + beg) // bpPerPix
   688                 e = div_ceil(origin + end, bpPerPix)
   689             else:
   690                 # exclude partly-covered pixels
   691                 b = div_ceil(origin + beg, bpPerPix)
   692                 e = (origin + end) // bpPerPix
   693                 if e <= b: continue
   694                 if bedEnd >= rangeEnd:  # include partly-covered end pixels
   695                     if isReverseRange:
   696                         b = (origin + beg) // bpPerPix
   697                     else:
   698                         e = div_ceil(origin + end, bpPerPix)
   699             if isTop:
   700                 box = b, margin, e, edge
   701             else:
   702                 box = margin, b, edge, e
   703             yield layer, color, box
   704 
   705 def drawAnnotations(im, boxes):
   706     # xxx use partial transparency for different-color overlaps?
   707     for layer, color, box in boxes:
   708         im.paste(color, box)
   709 
   710 def placedLabels(labels, rangePixBegs, rangePixLens, beg, end):
   711     '''Return axis labels with endpoint & sort-order information.'''
   712     maxWidth = end - beg
   713     for i, j, k in zip(labels, rangePixBegs, rangePixLens):
   714         text, textWidth, textHeight, strandNum = i
   715         if textWidth > maxWidth:
   716             continue
   717         labelBeg = j + (k - textWidth) // 2
   718         labelEnd = labelBeg + textWidth
   719         sortKey = textWidth - k
   720         if labelBeg < beg:
   721             sortKey += maxWidth * (beg - labelBeg)
   722             labelBeg = beg
   723             labelEnd = beg + textWidth
   724         if labelEnd > end:
   725             sortKey += maxWidth * (labelEnd - end)
   726             labelEnd = end
   727             labelBeg = end - textWidth
   728         yield sortKey, labelBeg, labelEnd, text, textHeight, strandNum
   729 
   730 def nonoverlappingLabels(labels, minPixTweenLabels):
   731     '''Get a subset of non-overlapping axis labels, greedily.'''
   732     out = []
   733     for i in labels:
   734         beg = i[1] - minPixTweenLabels
   735         end = i[2] + minPixTweenLabels
   736         if all(j[2] <= beg or j[1] >= end for j in out):
   737             out.append(i)
   738     return out
   739 
   740 def axisImage(labels, rangePixBegs, rangePixLens, textRot,
   741               textAln, font, image_mode, opts):
   742     '''Make an image of axis labels.'''
   743     beg = rangePixBegs[0]
   744     end = rangePixBegs[-1] + rangePixLens[-1]
   745     margin = max(i[2] for i in labels)
   746     labels = sorted(placedLabels(labels, rangePixBegs, rangePixLens, beg, end))
   747     minPixTweenLabels = 0 if textRot else opts.label_space
   748     labels = nonoverlappingLabels(labels, minPixTweenLabels)
   749     image_size = (margin, end) if textRot else (end, margin)
   750     im = Image.new(image_mode, image_size, opts.margin_color)
   751     draw = ImageDraw.Draw(im)
   752     for sortKey, labelBeg, labelEnd, text, textHeight, strandNum in labels:
   753         base = margin - textHeight if textAln else 0
   754         position = (base, labelBeg) if textRot else (labelBeg, base)
   755         fill = ("black", opts.forwardcolor, opts.reversecolor)[strandNum]
   756         draw.text(position, text, font=font, fill=fill)
   757     return im
   758 
   759 def rangesWithOrigins(sortedRanges, rangePixBegs, rangePixLens, bpPerPix):
   760     for i, j, k in zip(sortedRanges, rangePixBegs, rangePixLens):
   761         seqName, rangeBeg, rangeEnd, strandNum = i
   762         isReverseRange = (strandNum > 1)
   763         if isReverseRange:
   764             origin = bpPerPix * (j + k) + rangeBeg
   765         else:
   766             origin = bpPerPix * j - rangeBeg
   767         yield seqName, (rangeBeg, rangeEnd, isReverseRange, origin)
   768 
   769 def rangesAndOriginsPerSeq(sortedRanges, rangePixBegs, rangePixLens, bpPerPix):
   770     a = rangesWithOrigins(sortedRanges, rangePixBegs, rangePixLens, bpPerPix)
   771     for seqName, group in itertools.groupby(a, itemgetter(0)):
   772         yield seqName, sorted(i[1] for i in group)
   773 
   774 def getFont(opts):
   775     if opts.fontfile:
   776         return ImageFont.truetype(opts.fontfile, opts.fontsize)
   777     fileNames = []
   778     try:
   779         x = ["fc-match", "-f%{file}", "arial"]
   780         p = subprocess.Popen(x, stdout=subprocess.PIPE, stderr=subprocess.PIPE,
   781                              universal_newlines=True)
   782         out, err = p.communicate()
   783         fileNames.append(out)
   784     except OSError as e:
   785         logging.info("fc-match error: " + str(e))
   786     fileNames.append("/Library/Fonts/Arial.ttf")  # for Mac
   787     for i in fileNames:
   788         try:
   789             font = ImageFont.truetype(i, opts.fontsize)
   790             logging.info("font: " + i)
   791             return font
   792         except IOError as e:
   793             logging.info("font load error: " + str(e))
   794     return ImageFont.load_default()
   795 
   796 def sequenceSizesAndNames(seqRanges):
   797     for seqName, ranges in itertools.groupby(seqRanges, itemgetter(0)):
   798         size = sum(e - b for n, b, e in ranges)
   799         yield size, seqName
   800 
   801 def biggestSequences(seqRanges, maxNumOfSequences):
   802     s = sorted(sequenceSizesAndNames(seqRanges), reverse=True)
   803     if len(s) > maxNumOfSequences:
   804         logging.warning("too many sequences - discarding the smallest ones")
   805         s = s[:maxNumOfSequences]
   806     return set(i[1] for i in s)
   807 
   808 def remainingSequenceRanges(seqRanges, alignments, seqIndex):
   809     remainingSequences = set(i[seqIndex] for i in alignments)
   810     return [i for i in seqRanges if i[0] in remainingSequences]
   811 
   812 def readAnnotations(opts, rangeDict, bedFile, repFile, geneFile, gapFile):
   813     annots = itertools.chain(readBed(bedFile, rangeDict),
   814                              readRmsk(repFile, rangeDict),
   815                              readGenePred(opts, geneFile, rangeDict),
   816                              readGaps(opts, gapFile, rangeDict))
   817     return annots
   818 
   819 def lastDotplot(opts, args):
   820     logLevel = logging.INFO if opts.verbose else logging.WARNING
   821     logging.basicConfig(format="%(filename)s: %(message)s", level=logLevel)
   822 
   823     font = getFont(opts)
   824     image_mode = 'RGB'
   825     forward_color = ImageColor.getcolor(opts.forwardcolor, image_mode)
   826     reverse_color = ImageColor.getcolor(opts.reversecolor, image_mode)
   827     zipped_colors = zip(forward_color, reverse_color)
   828     overlap_color = tuple([(i + j) // 2 for i, j in zipped_colors])
   829 
   830     maxGap1, maxGapB1 = twoValuesFromOption(opts.max_gap1, ":")
   831     maxGap2, maxGapB2 = twoValuesFromOption(opts.max_gap2, ":")
   832 
   833     logging.info("reading alignments...")
   834     alnData = readAlignments(args[0], opts)
   835     alignments, seqRanges1, coverDict1, seqRanges2, coverDict2 = alnData
   836     if not alignments: raise Exception("there are no alignments")
   837     logging.info("cutting...")
   838     coverDict1 = dict(mergedRangesPerSeq(coverDict1))
   839     coverDict2 = dict(mergedRangesPerSeq(coverDict2))
   840     minAlignedBases = min(coveredLength(coverDict1), coveredLength(coverDict2))
   841     pad = int(opts.pad * minAlignedBases)
   842     cutRanges1 = list(trimmed(seqRanges1, coverDict1, minAlignedBases,
   843                               maxGap1, pad, pad))
   844     cutRanges2 = list(trimmed(seqRanges2, coverDict2, minAlignedBases,
   845                               maxGap2, pad, pad))
   846 
   847     biggestSeqs1 = biggestSequences(cutRanges1, opts.maxseqs)
   848     cutRanges1 = [i for i in cutRanges1 if i[0] in biggestSeqs1]
   849     alignments = [i for i in alignments if i[0] in biggestSeqs1]
   850     cutRanges2 = remainingSequenceRanges(cutRanges2, alignments, 1)
   851 
   852     biggestSeqs2 = biggestSequences(cutRanges2, opts.maxseqs)
   853     cutRanges2 = [i for i in cutRanges2 if i[0] in biggestSeqs2]
   854     alignments = [i for i in alignments if i[1] in biggestSeqs2]
   855     cutRanges1 = remainingSequenceRanges(cutRanges1, alignments, 0)
   856 
   857     logging.info("reading secondary alignments...")
   858     alnDataB = readSecondaryAlignments(opts, cutRanges1, cutRanges2)
   859     alignmentsB, seqRangesB1, coverDictB1, seqRangesB2, coverDictB2 = alnDataB
   860     logging.info("cutting...")
   861     coverDictB1 = dict(mergedRangesPerSeq(coverDictB1))
   862     coverDictB2 = dict(mergedRangesPerSeq(coverDictB2))
   863     cutRangesB1 = trimmed(seqRangesB1, coverDictB1, minAlignedBases,
   864                           maxGapB1, 0, 0)
   865     cutRangesB2 = trimmed(seqRangesB2, coverDictB2, minAlignedBases,
   866                           maxGapB2, 0, 0)
   867 
   868     logging.info("sorting...")
   869     sortOut = allSortedRanges(opts, alignments, alignmentsB,
   870                               cutRanges1, cutRangesB1, cutRanges2, cutRangesB2)
   871     sortedRanges1, sortedRanges2 = sortOut
   872 
   873     textDraw = None
   874     if opts.fontsize:
   875         textDraw = ImageDraw.Draw(Image.new(image_mode, (1, 1)))
   876 
   877     textRot1 = "vertical".startswith(opts.rot1)
   878     i1 = dataFromRanges(sortedRanges1, font, textDraw, opts.labels1, textRot1)
   879     rangeSizes1, labelData1, tMargin = i1
   880 
   881     textRot2 = "horizontal".startswith(opts.rot2)
   882     i2 = dataFromRanges(sortedRanges2, font, textDraw, opts.labels2, textRot2)
   883     rangeSizes2, labelData2, lMargin = i2
   884 
   885     maxPixels1 = opts.width  - lMargin
   886     maxPixels2 = opts.height - tMargin
   887     bpPerPix1 = get_bp_per_pix(rangeSizes1, opts.border_pixels, maxPixels1)
   888     bpPerPix2 = get_bp_per_pix(rangeSizes2, opts.border_pixels, maxPixels2)
   889     bpPerPix = max(bpPerPix1, bpPerPix2)
   890     logging.info("bp per pixel = " + str(bpPerPix))
   891 
   892     p1 = pixelData(rangeSizes1, bpPerPix, opts.border_pixels, lMargin)
   893     rangePixBegs1, rangePixLens1, width = p1
   894     rangeDict1 = dict(rangesAndOriginsPerSeq(sortedRanges1, rangePixBegs1,
   895                                              rangePixLens1, bpPerPix))
   896 
   897     p2 = pixelData(rangeSizes2, bpPerPix, opts.border_pixels, tMargin)
   898     rangePixBegs2, rangePixLens2, height = p2
   899     rangeDict2 = dict(rangesAndOriginsPerSeq(sortedRanges2, rangePixBegs2,
   900                                              rangePixLens2, bpPerPix))
   901 
   902     logging.info("width:  " + str(width))
   903     logging.info("height: " + str(height))
   904 
   905     logging.info("processing alignments...")
   906     allAlignments = alignments + alignmentsB
   907     hits = alignmentPixels(width, height, allAlignments, bpPerPix,
   908                            rangeDict1, rangeDict2)
   909 
   910     logging.info("reading annotations...")
   911 
   912     rangeDict1 = expandedSeqDict(rangeDict1)
   913     annots1 = readAnnotations(opts, rangeDict1,
   914                               opts.bed1, opts.rmsk1, opts.genePred1, opts.gap1)
   915     boxes1 = bedBoxes(annots1, rangeDict1, tMargin, height, True, bpPerPix)
   916 
   917     rangeDict2 = expandedSeqDict(rangeDict2)
   918     annots2 = readAnnotations(opts, rangeDict2,
   919                               opts.bed2, opts.rmsk2, opts.genePred2, opts.gap2)
   920     boxes2 = bedBoxes(annots2, rangeDict2, lMargin, width, False, bpPerPix)
   921 
   922     boxes = sorted(itertools.chain(boxes1, boxes2))
   923 
   924     logging.info("drawing...")
   925 
   926     image_size = width, height
   927     im = Image.new(image_mode, image_size, opts.background_color)
   928 
   929     drawAnnotations(im, boxes)
   930 
   931     joinA, joinB = twoValuesFromOption(opts.join, ":")
   932     if joinA in "13":
   933         drawJoins(im, alignments, bpPerPix, 0, rangeDict1, rangeDict2)
   934     if joinB in "13":
   935         drawJoins(im, alignmentsB, bpPerPix, 0, rangeDict1, rangeDict2)
   936     if joinA in "23":
   937         drawJoins(im, alignments, bpPerPix, 1, rangeDict2, rangeDict1)
   938     if joinB in "23":
   939         drawJoins(im, alignmentsB, bpPerPix, 1, rangeDict2, rangeDict1)
   940 
   941     for i in range(height):
   942         for j in range(width):
   943             store_value = hits[i * width + j]
   944             xy = j, i
   945             if   store_value == 1: im.putpixel(xy, forward_color)
   946             elif store_value == 2: im.putpixel(xy, reverse_color)
   947             elif store_value == 3: im.putpixel(xy, overlap_color)
   948 
   949     if opts.fontsize != 0:
   950         axis1 = axisImage(labelData1, rangePixBegs1, rangePixLens1,
   951                           textRot1, False, font, image_mode, opts)
   952         if textRot1:
   953             axis1 = axis1.transpose(Image.ROTATE_90)
   954         axis2 = axisImage(labelData2, rangePixBegs2, rangePixLens2,
   955                           textRot2, textRot2, font, image_mode, opts)
   956         if not textRot2:
   957             axis2 = axis2.transpose(Image.ROTATE_270)
   958         im.paste(axis1, (0, 0))
   959         im.paste(axis2, (0, 0))
   960 
   961     for i in rangePixBegs1[1:]:
   962         box = i - opts.border_pixels, tMargin, i, height
   963         im.paste(opts.border_color, box)
   964 
   965     for i in rangePixBegs2[1:]:
   966         box = lMargin, i - opts.border_pixels, width, i
   967         im.paste(opts.border_color, box)
   968 
   969     im.save(args[1])
   970 
   971 if __name__ == "__main__":
   972     usage = """%prog --help
   973    or: %prog [options] maf-or-tab-alignments dotplot.png
   974    or: %prog [options] maf-or-tab-alignments dotplot.gif
   975    or: ..."""
   976     description = "Draw a dotplot of pair-wise sequence alignments in MAF or tabular format."
   977     op = optparse.OptionParser(usage=usage, description=description)
   978     op.add_option("-v", "--verbose", action="count",
   979                   help="show progress messages & data about the plot")
   980     # Replace "width" & "height" with a single "length" option?
   981     op.add_option("-x", "--width", metavar="INT", type="int", default=1000,
   982                   help="maximum width in pixels (default: %default)")
   983     op.add_option("-y", "--height", metavar="INT", type="int", default=1000,
   984                   help="maximum height in pixels (default: %default)")
   985     op.add_option("-m", "--maxseqs", type="int", default=100, metavar="M",
   986                   help="maximum number of horizontal or vertical sequences "
   987                   "(default=%default)")
   988     op.add_option("-1", "--seq1", metavar="PATTERN", action="append",
   989                   default=[],
   990                   help="which sequences to show from the 1st genome")
   991     op.add_option("-2", "--seq2", metavar="PATTERN", action="append",
   992                   default=[],
   993                   help="which sequences to show from the 2nd genome")
   994     op.add_option("-c", "--forwardcolor", metavar="COLOR", default="red",
   995                   help="color for forward alignments (default: %default)")
   996     op.add_option("-r", "--reversecolor", metavar="COLOR", default="blue",
   997                   help="color for reverse alignments (default: %default)")
   998     op.add_option("--alignments", metavar="FILE", help="secondary alignments")
   999     op.add_option("--sort1", default="1", metavar="N",
  1000                   help="genome1 sequence order: 0=input order, 1=name order, "
  1001                   "2=length order, 3=alignment order (default=%default)")
  1002     op.add_option("--sort2", default="1", metavar="N",
  1003                   help="genome2 sequence order: 0=input order, 1=name order, "
  1004                   "2=length order, 3=alignment order (default=%default)")
  1005     op.add_option("--strands1", default="0", metavar="N", help=
  1006                   "genome1 sequence orientation: 0=forward orientation, "
  1007                   "1=alignment orientation (default=%default)")
  1008     op.add_option("--strands2", default="0", metavar="N", help=
  1009                   "genome2 sequence orientation: 0=forward orientation, "
  1010                   "1=alignment orientation (default=%default)")
  1011     op.add_option("--max-gap1", metavar="FRAC", default="0.5,2", help=
  1012                   "maximum unaligned (end,mid) gap in genome1: "
  1013                   "fraction of aligned length (default=%default)")
  1014     op.add_option("--max-gap2", metavar="FRAC", default="0.5,2", help=
  1015                   "maximum unaligned (end,mid) gap in genome2: "
  1016                   "fraction of aligned length (default=%default)")
  1017     op.add_option("--pad", metavar="FRAC", type="float", default=0.04, help=
  1018                   "pad length when cutting unaligned gaps: "
  1019                   "fraction of aligned length (default=%default)")
  1020     op.add_option("-j", "--join", default="0", metavar="N", help=
  1021                   "join: 0=nothing, 1=alignments adjacent in genome1, "
  1022                   "2=alignments adjacent in genome2 (default=%default)")
  1023     op.add_option("--border-pixels", metavar="INT", type="int", default=1,
  1024                   help="number of pixels between sequences (default=%default)")
  1025     op.add_option("--border-color", metavar="COLOR", default="black",
  1026                   help="color for pixels between sequences (default=%default)")
  1027     # --break-color and/or --break-pixels for intra-sequence breaks?
  1028     op.add_option("--margin-color", metavar="COLOR", default="#dcdcdc",
  1029                   help="margin color")
  1030 
  1031     og = optparse.OptionGroup(op, "Text options")
  1032     og.add_option("-f", "--fontfile", metavar="FILE",
  1033                   help="TrueType or OpenType font file")
  1034     og.add_option("-s", "--fontsize", metavar="SIZE", type="int", default=14,
  1035                   help="TrueType or OpenType font size (default: %default)")
  1036     og.add_option("--labels1", type="int", default=0, metavar="N", help=
  1037                   "genome1 labels: 0=name, 1=name:length, "
  1038                   "2=name:start:length, 3=name:start-end (default=%default)")
  1039     og.add_option("--labels2", type="int", default=0, metavar="N", help=
  1040                   "genome2 labels: 0=name, 1=name:length, "
  1041                   "2=name:start:length, 3=name:start-end (default=%default)")
  1042     og.add_option("--rot1", metavar="ROT", default="h",
  1043                   help="text rotation for the 1st genome (default=%default)")
  1044     og.add_option("--rot2", metavar="ROT", default="v",
  1045                   help="text rotation for the 2nd genome (default=%default)")
  1046     op.add_option_group(og)
  1047 
  1048     og = optparse.OptionGroup(op, "Annotation options")
  1049     og.add_option("--bed1", metavar="FILE",
  1050                   help="read genome1 annotations from BED file")
  1051     og.add_option("--bed2", metavar="FILE",
  1052                   help="read genome2 annotations from BED file")
  1053     og.add_option("--rmsk1", metavar="FILE", help="read genome1 repeats from "
  1054                   "RepeatMasker .out or rmsk.txt file")
  1055     og.add_option("--rmsk2", metavar="FILE", help="read genome2 repeats from "
  1056                   "RepeatMasker .out or rmsk.txt file")
  1057     op.add_option_group(og)
  1058 
  1059     og = optparse.OptionGroup(op, "Gene options")
  1060     og.add_option("--genePred1", metavar="FILE",
  1061                   help="read genome1 genes from genePred file")
  1062     og.add_option("--genePred2", metavar="FILE",
  1063                   help="read genome2 genes from genePred file")
  1064     og.add_option("--exon-color", metavar="COLOR", default="PaleGreen",
  1065                   help="color for exons (default=%default)")
  1066     og.add_option("--cds-color", metavar="COLOR", default="LimeGreen",
  1067                   help="color for protein-coding regions (default=%default)")
  1068     op.add_option_group(og)
  1069 
  1070     og = optparse.OptionGroup(op, "Unsequenced gap options")
  1071     og.add_option("--gap1", metavar="FILE",
  1072                   help="read genome1 unsequenced gaps from agp or gap file")
  1073     og.add_option("--gap2", metavar="FILE",
  1074                   help="read genome2 unsequenced gaps from agp or gap file")
  1075     og.add_option("--bridged-color", metavar="COLOR", default="yellow",
  1076                   help="color for bridged gaps (default: %default)")
  1077     og.add_option("--unbridged-color", metavar="COLOR", default="orange",
  1078                   help="color for unbridged gaps (default: %default)")
  1079     op.add_option_group(og)
  1080     (opts, args) = op.parse_args()
  1081     if len(args) != 2: op.error("2 arguments needed")
  1082 
  1083     opts.background_color = "white"
  1084     opts.label_space = 5     # minimum number of pixels between axis labels
  1085 
  1086     try: lastDotplot(opts, args)
  1087     except KeyboardInterrupt: pass  # avoid silly error message
  1088     except Exception as e:
  1089         prog = os.path.basename(sys.argv[0])
  1090         sys.exit(prog + ": error: " + str(e))