scripts/last-dotplot
author Martin C. Frith
Thu Jul 30 21:14:13 2020 +0900 (21 months ago)
changeset 1068 a29f9cec16e1
parent 1062 6d8d56a74b14
child 1069 da8b081ec496
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 "+-": fields = fields[1:]
   618         seqName = fields[1]
   619         if seqName not in rangeDict: continue
   620         #strand = fields[2]
   621         cdsBeg = int(fields[5])
   622         cdsEnd = int(fields[6])
   623         exonBegs = commaSeparatedInts(fields[8])
   624         exonEnds = commaSeparatedInts(fields[9])
   625         for beg, end in zip(exonBegs, exonEnds):
   626             yield 300, opts.exon_color, seqName, beg, end
   627             b = max(beg, cdsBeg)
   628             e = min(end, cdsEnd)
   629             if b < e: yield 400, opts.cds_color, seqName, b, e
   630 
   631 def readRmsk(fileName, rangeDict):
   632     for line in myOpen(fileName):
   633         fields = line.split()
   634         if len(fields) == 17:  # rmsk.txt
   635             seqName = fields[5]
   636             if seqName not in rangeDict: continue  # do this ASAP for speed
   637             beg = int(fields[6])
   638             end = int(fields[7])
   639             strand = fields[9]
   640             repeatClass = fields[11]
   641         elif len(fields) == 15:  # .out
   642             seqName = fields[4]
   643             if seqName not in rangeDict: continue
   644             beg = int(fields[5]) - 1
   645             end = int(fields[6])
   646             strand = fields[8]
   647             repeatClass = fields[10].split("/")[0]
   648         else:
   649             continue
   650         if repeatClass in ("Low_complexity", "Simple_repeat", "Satellite"):
   651             yield 200, "#fbf", seqName, beg, end
   652         elif (strand == "+") != rangeDict[seqName][0][2]:
   653             yield 100, "#ffe8e8", seqName, beg, end
   654         else:
   655             yield 100, "#e8e8ff", seqName, beg, end
   656 
   657 def isExtraFirstGapField(fields):
   658     return fields[4].isdigit()
   659 
   660 def readGaps(opts, fileName, rangeDict):
   661     '''Read locations of unsequenced gaps, from an agp or gap file.'''
   662     for line in myOpen(fileName):
   663         w = line.split()
   664         if not w or w[0][0] == "#": continue
   665         if isExtraFirstGapField(w): w = w[1:]
   666         if w[4] not in "NU": continue
   667         seqName = w[0]
   668         if seqName not in rangeDict: continue
   669         end = int(w[2])
   670         beg = end - int(w[5])  # zero-based coordinate
   671         if w[7] == "yes":
   672             yield 3000, opts.bridged_color, seqName, beg, end
   673         else:
   674             yield 2000, opts.unbridged_color, seqName, beg, end
   675 
   676 def bedBoxes(beds, rangeDict, margin, edge, isTop, bpPerPix):
   677     for layer, color, seqName, bedBeg, bedEnd in beds:
   678         for rangeBeg, rangeEnd, isReverseRange, origin in rangeDict[seqName]:
   679             beg = max(bedBeg, rangeBeg)
   680             end = min(bedEnd, rangeEnd)
   681             if beg >= end: continue
   682             if isReverseRange:
   683                 beg, end = -end, -beg
   684             if layer <= 1000:
   685                 # include partly-covered pixels
   686                 b = (origin + beg) // bpPerPix
   687                 e = div_ceil(origin + end, bpPerPix)
   688             else:
   689                 # exclude partly-covered pixels
   690                 b = div_ceil(origin + beg, bpPerPix)
   691                 e = (origin + end) // bpPerPix
   692                 if e <= b: continue
   693                 if bedEnd >= rangeEnd:  # include partly-covered end pixels
   694                     if isReverseRange:
   695                         b = (origin + beg) // bpPerPix
   696                     else:
   697                         e = div_ceil(origin + end, bpPerPix)
   698             if isTop:
   699                 box = b, margin, e, edge
   700             else:
   701                 box = margin, b, edge, e
   702             yield layer, color, box
   703 
   704 def drawAnnotations(im, boxes):
   705     # xxx use partial transparency for different-color overlaps?
   706     for layer, color, box in boxes:
   707         im.paste(color, box)
   708 
   709 def placedLabels(labels, rangePixBegs, rangePixLens, beg, end):
   710     '''Return axis labels with endpoint & sort-order information.'''
   711     maxWidth = end - beg
   712     for i, j, k in zip(labels, rangePixBegs, rangePixLens):
   713         text, textWidth, textHeight, strandNum = i
   714         if textWidth > maxWidth:
   715             continue
   716         labelBeg = j + (k - textWidth) // 2
   717         labelEnd = labelBeg + textWidth
   718         sortKey = textWidth - k
   719         if labelBeg < beg:
   720             sortKey += maxWidth * (beg - labelBeg)
   721             labelBeg = beg
   722             labelEnd = beg + textWidth
   723         if labelEnd > end:
   724             sortKey += maxWidth * (labelEnd - end)
   725             labelEnd = end
   726             labelBeg = end - textWidth
   727         yield sortKey, labelBeg, labelEnd, text, textHeight, strandNum
   728 
   729 def nonoverlappingLabels(labels, minPixTweenLabels):
   730     '''Get a subset of non-overlapping axis labels, greedily.'''
   731     out = []
   732     for i in labels:
   733         beg = i[1] - minPixTweenLabels
   734         end = i[2] + minPixTweenLabels
   735         if all(j[2] <= beg or j[1] >= end for j in out):
   736             out.append(i)
   737     return out
   738 
   739 def axisImage(labels, rangePixBegs, rangePixLens, textRot,
   740               textAln, font, image_mode, opts):
   741     '''Make an image of axis labels.'''
   742     beg = rangePixBegs[0]
   743     end = rangePixBegs[-1] + rangePixLens[-1]
   744     margin = max(i[2] for i in labels)
   745     labels = sorted(placedLabels(labels, rangePixBegs, rangePixLens, beg, end))
   746     minPixTweenLabels = 0 if textRot else opts.label_space
   747     labels = nonoverlappingLabels(labels, minPixTweenLabels)
   748     image_size = (margin, end) if textRot else (end, margin)
   749     im = Image.new(image_mode, image_size, opts.margin_color)
   750     draw = ImageDraw.Draw(im)
   751     for sortKey, labelBeg, labelEnd, text, textHeight, strandNum in labels:
   752         base = margin - textHeight if textAln else 0
   753         position = (base, labelBeg) if textRot else (labelBeg, base)
   754         fill = ("black", opts.forwardcolor, opts.reversecolor)[strandNum]
   755         draw.text(position, text, font=font, fill=fill)
   756     return im
   757 
   758 def rangesWithOrigins(sortedRanges, rangePixBegs, rangePixLens, bpPerPix):
   759     for i, j, k in zip(sortedRanges, rangePixBegs, rangePixLens):
   760         seqName, rangeBeg, rangeEnd, strandNum = i
   761         isReverseRange = (strandNum > 1)
   762         if isReverseRange:
   763             origin = bpPerPix * (j + k) + rangeBeg
   764         else:
   765             origin = bpPerPix * j - rangeBeg
   766         yield seqName, (rangeBeg, rangeEnd, isReverseRange, origin)
   767 
   768 def rangesPerSeq(sortedRanges, rangePixBegs, rangePixLens, bpPerPix):
   769     a = rangesWithOrigins(sortedRanges, rangePixBegs, rangePixLens, bpPerPix)
   770     for k, v in itertools.groupby(a, itemgetter(0)):
   771         yield k, sorted(i[1] for i in v)
   772 
   773 def getFont(opts):
   774     if opts.fontfile:
   775         return ImageFont.truetype(opts.fontfile, opts.fontsize)
   776     fileNames = []
   777     try:
   778         x = ["fc-match", "-f%{file}", "arial"]
   779         p = subprocess.Popen(x, stdout=subprocess.PIPE, stderr=subprocess.PIPE,
   780                              universal_newlines=True)
   781         out, err = p.communicate()
   782         fileNames.append(out)
   783     except OSError as e:
   784         logging.info("fc-match error: " + str(e))
   785     fileNames.append("/Library/Fonts/Arial.ttf")  # for Mac
   786     for i in fileNames:
   787         try:
   788             font = ImageFont.truetype(i, opts.fontsize)
   789             logging.info("font: " + i)
   790             return font
   791         except IOError as e:
   792             logging.info("font load error: " + str(e))
   793     return ImageFont.load_default()
   794 
   795 def sequenceSizesAndNames(seqRanges):
   796     for seqName, ranges in itertools.groupby(seqRanges, itemgetter(0)):
   797         size = sum(e - b for n, b, e in ranges)
   798         yield size, seqName
   799 
   800 def biggestSequences(seqRanges, maxNumOfSequences):
   801     s = sorted(sequenceSizesAndNames(seqRanges), reverse=True)
   802     if len(s) > maxNumOfSequences:
   803         logging.warning("too many sequences - discarding the smallest ones")
   804         s = s[:maxNumOfSequences]
   805     return set(i[1] for i in s)
   806 
   807 def remainingSequenceRanges(seqRanges, alignments, seqIndex):
   808     remainingSequences = set(i[seqIndex] for i in alignments)
   809     return [i for i in seqRanges if i[0] in remainingSequences]
   810 
   811 def lastDotplot(opts, args):
   812     logLevel = logging.INFO if opts.verbose else logging.WARNING
   813     logging.basicConfig(format="%(filename)s: %(message)s", level=logLevel)
   814 
   815     font = getFont(opts)
   816     image_mode = 'RGB'
   817     forward_color = ImageColor.getcolor(opts.forwardcolor, image_mode)
   818     reverse_color = ImageColor.getcolor(opts.reversecolor, image_mode)
   819     zipped_colors = zip(forward_color, reverse_color)
   820     overlap_color = tuple([(i + j) // 2 for i, j in zipped_colors])
   821 
   822     maxGap1, maxGapB1 = twoValuesFromOption(opts.max_gap1, ":")
   823     maxGap2, maxGapB2 = twoValuesFromOption(opts.max_gap2, ":")
   824 
   825     logging.info("reading alignments...")
   826     alnData = readAlignments(args[0], opts)
   827     alignments, seqRanges1, coverDict1, seqRanges2, coverDict2 = alnData
   828     if not alignments: raise Exception("there are no alignments")
   829     logging.info("cutting...")
   830     coverDict1 = dict(mergedRangesPerSeq(coverDict1))
   831     coverDict2 = dict(mergedRangesPerSeq(coverDict2))
   832     minAlignedBases = min(coveredLength(coverDict1), coveredLength(coverDict2))
   833     pad = int(opts.pad * minAlignedBases)
   834     cutRanges1 = list(trimmed(seqRanges1, coverDict1, minAlignedBases,
   835                               maxGap1, pad, pad))
   836     cutRanges2 = list(trimmed(seqRanges2, coverDict2, minAlignedBases,
   837                               maxGap2, pad, pad))
   838 
   839     biggestSeqs1 = biggestSequences(cutRanges1, opts.maxseqs)
   840     cutRanges1 = [i for i in cutRanges1 if i[0] in biggestSeqs1]
   841     alignments = [i for i in alignments if i[0] in biggestSeqs1]
   842     cutRanges2 = remainingSequenceRanges(cutRanges2, alignments, 1)
   843 
   844     biggestSeqs2 = biggestSequences(cutRanges2, opts.maxseqs)
   845     cutRanges2 = [i for i in cutRanges2 if i[0] in biggestSeqs2]
   846     alignments = [i for i in alignments if i[1] in biggestSeqs2]
   847     cutRanges1 = remainingSequenceRanges(cutRanges1, alignments, 0)
   848 
   849     logging.info("reading secondary alignments...")
   850     alnDataB = readSecondaryAlignments(opts, cutRanges1, cutRanges2)
   851     alignmentsB, seqRangesB1, coverDictB1, seqRangesB2, coverDictB2 = alnDataB
   852     logging.info("cutting...")
   853     coverDictB1 = dict(mergedRangesPerSeq(coverDictB1))
   854     coverDictB2 = dict(mergedRangesPerSeq(coverDictB2))
   855     cutRangesB1 = trimmed(seqRangesB1, coverDictB1, minAlignedBases,
   856                           maxGapB1, 0, 0)
   857     cutRangesB2 = trimmed(seqRangesB2, coverDictB2, minAlignedBases,
   858                           maxGapB2, 0, 0)
   859 
   860     logging.info("sorting...")
   861     sortOut = allSortedRanges(opts, alignments, alignmentsB,
   862                               cutRanges1, cutRangesB1, cutRanges2, cutRangesB2)
   863     sortedRanges1, sortedRanges2 = sortOut
   864 
   865     textDraw = None
   866     if opts.fontsize:
   867         textDraw = ImageDraw.Draw(Image.new(image_mode, (1, 1)))
   868 
   869     textRot1 = "vertical".startswith(opts.rot1)
   870     i1 = dataFromRanges(sortedRanges1, font, textDraw, opts.labels1, textRot1)
   871     rangeSizes1, labelData1, tMargin = i1
   872 
   873     textRot2 = "horizontal".startswith(opts.rot2)
   874     i2 = dataFromRanges(sortedRanges2, font, textDraw, opts.labels2, textRot2)
   875     rangeSizes2, labelData2, lMargin = i2
   876 
   877     maxPixels1 = opts.width  - lMargin
   878     maxPixels2 = opts.height - tMargin
   879     bpPerPix1 = get_bp_per_pix(rangeSizes1, opts.border_pixels, maxPixels1)
   880     bpPerPix2 = get_bp_per_pix(rangeSizes2, opts.border_pixels, maxPixels2)
   881     bpPerPix = max(bpPerPix1, bpPerPix2)
   882     logging.info("bp per pixel = " + str(bpPerPix))
   883 
   884     p1 = pixelData(rangeSizes1, bpPerPix, opts.border_pixels, lMargin)
   885     rangePixBegs1, rangePixLens1, width = p1
   886     rangeDict1 = dict(rangesPerSeq(sortedRanges1, rangePixBegs1,
   887                                    rangePixLens1, bpPerPix))
   888 
   889     p2 = pixelData(rangeSizes2, bpPerPix, opts.border_pixels, tMargin)
   890     rangePixBegs2, rangePixLens2, height = p2
   891     rangeDict2 = dict(rangesPerSeq(sortedRanges2, rangePixBegs2,
   892                                    rangePixLens2, bpPerPix))
   893 
   894     logging.info("width:  " + str(width))
   895     logging.info("height: " + str(height))
   896 
   897     logging.info("processing alignments...")
   898     allAlignments = alignments + alignmentsB
   899     hits = alignmentPixels(width, height, allAlignments, bpPerPix,
   900                            rangeDict1, rangeDict2)
   901 
   902     logging.info("reading annotations...")
   903 
   904     rangeDict1 = expandedSeqDict(rangeDict1)
   905     beds1 = itertools.chain(readBed(opts.bed1, rangeDict1),
   906                             readRmsk(opts.rmsk1, rangeDict1),
   907                             readGenePred(opts, opts.genePred1, rangeDict1),
   908                             readGaps(opts, opts.gap1, rangeDict1))
   909     b1 = bedBoxes(beds1, rangeDict1, tMargin, height, True, bpPerPix)
   910 
   911     rangeDict2 = expandedSeqDict(rangeDict2)
   912     beds2 = itertools.chain(readBed(opts.bed2, rangeDict2),
   913                             readRmsk(opts.rmsk2, rangeDict2),
   914                             readGenePred(opts, opts.genePred2, rangeDict2),
   915                             readGaps(opts, opts.gap2, rangeDict2))
   916     b2 = bedBoxes(beds2, rangeDict2, lMargin, width, False, bpPerPix)
   917 
   918     boxes = sorted(itertools.chain(b1, b2))
   919 
   920     logging.info("drawing...")
   921 
   922     image_size = width, height
   923     im = Image.new(image_mode, image_size, opts.background_color)
   924 
   925     drawAnnotations(im, boxes)
   926 
   927     joinA, joinB = twoValuesFromOption(opts.join, ":")
   928     if joinA in "13":
   929         drawJoins(im, alignments, bpPerPix, 0, rangeDict1, rangeDict2)
   930     if joinB in "13":
   931         drawJoins(im, alignmentsB, bpPerPix, 0, rangeDict1, rangeDict2)
   932     if joinA in "23":
   933         drawJoins(im, alignments, bpPerPix, 1, rangeDict2, rangeDict1)
   934     if joinB in "23":
   935         drawJoins(im, alignmentsB, bpPerPix, 1, rangeDict2, rangeDict1)
   936 
   937     for i in range(height):
   938         for j in range(width):
   939             store_value = hits[i * width + j]
   940             xy = j, i
   941             if   store_value == 1: im.putpixel(xy, forward_color)
   942             elif store_value == 2: im.putpixel(xy, reverse_color)
   943             elif store_value == 3: im.putpixel(xy, overlap_color)
   944 
   945     if opts.fontsize != 0:
   946         axis1 = axisImage(labelData1, rangePixBegs1, rangePixLens1,
   947                           textRot1, False, font, image_mode, opts)
   948         if textRot1:
   949             axis1 = axis1.transpose(Image.ROTATE_90)
   950         axis2 = axisImage(labelData2, rangePixBegs2, rangePixLens2,
   951                           textRot2, textRot2, font, image_mode, opts)
   952         if not textRot2:
   953             axis2 = axis2.transpose(Image.ROTATE_270)
   954         im.paste(axis1, (0, 0))
   955         im.paste(axis2, (0, 0))
   956 
   957     for i in rangePixBegs1[1:]:
   958         box = i - opts.border_pixels, tMargin, i, height
   959         im.paste(opts.border_color, box)
   960 
   961     for i in rangePixBegs2[1:]:
   962         box = lMargin, i - opts.border_pixels, width, i
   963         im.paste(opts.border_color, box)
   964 
   965     im.save(args[1])
   966 
   967 if __name__ == "__main__":
   968     usage = """%prog --help
   969    or: %prog [options] maf-or-tab-alignments dotplot.png
   970    or: %prog [options] maf-or-tab-alignments dotplot.gif
   971    or: ..."""
   972     description = "Draw a dotplot of pair-wise sequence alignments in MAF or tabular format."
   973     op = optparse.OptionParser(usage=usage, description=description)
   974     op.add_option("-v", "--verbose", action="count",
   975                   help="show progress messages & data about the plot")
   976     # Replace "width" & "height" with a single "length" option?
   977     op.add_option("-x", "--width", metavar="INT", type="int", default=1000,
   978                   help="maximum width in pixels (default: %default)")
   979     op.add_option("-y", "--height", metavar="INT", type="int", default=1000,
   980                   help="maximum height in pixels (default: %default)")
   981     op.add_option("-m", "--maxseqs", type="int", default=100, metavar="M",
   982                   help="maximum number of horizontal or vertical sequences "
   983                   "(default=%default)")
   984     op.add_option("-1", "--seq1", metavar="PATTERN", action="append",
   985                   default=[],
   986                   help="which sequences to show from the 1st genome")
   987     op.add_option("-2", "--seq2", metavar="PATTERN", action="append",
   988                   default=[],
   989                   help="which sequences to show from the 2nd genome")
   990     op.add_option("-c", "--forwardcolor", metavar="COLOR", default="red",
   991                   help="color for forward alignments (default: %default)")
   992     op.add_option("-r", "--reversecolor", metavar="COLOR", default="blue",
   993                   help="color for reverse alignments (default: %default)")
   994     op.add_option("--alignments", metavar="FILE", help="secondary alignments")
   995     op.add_option("--sort1", default="1", metavar="N",
   996                   help="genome1 sequence order: 0=input order, 1=name order, "
   997                   "2=length order, 3=alignment order (default=%default)")
   998     op.add_option("--sort2", default="1", metavar="N",
   999                   help="genome2 sequence order: 0=input order, 1=name order, "
  1000                   "2=length order, 3=alignment order (default=%default)")
  1001     op.add_option("--strands1", default="0", metavar="N", help=
  1002                   "genome1 sequence orientation: 0=forward orientation, "
  1003                   "1=alignment orientation (default=%default)")
  1004     op.add_option("--strands2", default="0", metavar="N", help=
  1005                   "genome2 sequence orientation: 0=forward orientation, "
  1006                   "1=alignment orientation (default=%default)")
  1007     op.add_option("--max-gap1", metavar="FRAC", default="0.5,2", help=
  1008                   "maximum unaligned (end,mid) gap in genome1: "
  1009                   "fraction of aligned length (default=%default)")
  1010     op.add_option("--max-gap2", metavar="FRAC", default="0.5,2", help=
  1011                   "maximum unaligned (end,mid) gap in genome2: "
  1012                   "fraction of aligned length (default=%default)")
  1013     op.add_option("--pad", metavar="FRAC", type="float", default=0.04, help=
  1014                   "pad length when cutting unaligned gaps: "
  1015                   "fraction of aligned length (default=%default)")
  1016     op.add_option("-j", "--join", default="0", metavar="N", help=
  1017                   "join: 0=nothing, 1=alignments adjacent in genome1, "
  1018                   "2=alignments adjacent in genome2 (default=%default)")
  1019     op.add_option("--border-pixels", metavar="INT", type="int", default=1,
  1020                   help="number of pixels between sequences (default=%default)")
  1021     op.add_option("--border-color", metavar="COLOR", default="black",
  1022                   help="color for pixels between sequences (default=%default)")
  1023     # --break-color and/or --break-pixels for intra-sequence breaks?
  1024     op.add_option("--margin-color", metavar="COLOR", default="#dcdcdc",
  1025                   help="margin color")
  1026 
  1027     og = optparse.OptionGroup(op, "Text options")
  1028     og.add_option("-f", "--fontfile", metavar="FILE",
  1029                   help="TrueType or OpenType font file")
  1030     og.add_option("-s", "--fontsize", metavar="SIZE", type="int", default=14,
  1031                   help="TrueType or OpenType font size (default: %default)")
  1032     og.add_option("--labels1", type="int", default=0, metavar="N", help=
  1033                   "genome1 labels: 0=name, 1=name:length, "
  1034                   "2=name:start:length, 3=name:start-end (default=%default)")
  1035     og.add_option("--labels2", type="int", default=0, metavar="N", help=
  1036                   "genome2 labels: 0=name, 1=name:length, "
  1037                   "2=name:start:length, 3=name:start-end (default=%default)")
  1038     og.add_option("--rot1", metavar="ROT", default="h",
  1039                   help="text rotation for the 1st genome (default=%default)")
  1040     og.add_option("--rot2", metavar="ROT", default="v",
  1041                   help="text rotation for the 2nd genome (default=%default)")
  1042     op.add_option_group(og)
  1043 
  1044     og = optparse.OptionGroup(op, "Annotation options")
  1045     og.add_option("--bed1", metavar="FILE",
  1046                   help="read genome1 annotations from BED file")
  1047     og.add_option("--bed2", metavar="FILE",
  1048                   help="read genome2 annotations from BED file")
  1049     og.add_option("--rmsk1", metavar="FILE", help="read genome1 repeats from "
  1050                   "RepeatMasker .out or rmsk.txt file")
  1051     og.add_option("--rmsk2", metavar="FILE", help="read genome2 repeats from "
  1052                   "RepeatMasker .out or rmsk.txt file")
  1053     op.add_option_group(og)
  1054 
  1055     og = optparse.OptionGroup(op, "Gene options")
  1056     og.add_option("--genePred1", metavar="FILE",
  1057                   help="read genome1 genes from genePred file")
  1058     og.add_option("--genePred2", metavar="FILE",
  1059                   help="read genome2 genes from genePred file")
  1060     og.add_option("--exon-color", metavar="COLOR", default="PaleGreen",
  1061                   help="color for exons (default=%default)")
  1062     og.add_option("--cds-color", metavar="COLOR", default="LimeGreen",
  1063                   help="color for protein-coding regions (default=%default)")
  1064     op.add_option_group(og)
  1065 
  1066     og = optparse.OptionGroup(op, "Unsequenced gap options")
  1067     og.add_option("--gap1", metavar="FILE",
  1068                   help="read genome1 unsequenced gaps from agp or gap file")
  1069     og.add_option("--gap2", metavar="FILE",
  1070                   help="read genome2 unsequenced gaps from agp or gap file")
  1071     og.add_option("--bridged-color", metavar="COLOR", default="yellow",
  1072                   help="color for bridged gaps (default: %default)")
  1073     og.add_option("--unbridged-color", metavar="COLOR", default="orange",
  1074                   help="color for unbridged gaps (default: %default)")
  1075     op.add_option_group(og)
  1076     (opts, args) = op.parse_args()
  1077     if len(args) != 2: op.error("2 arguments needed")
  1078 
  1079     opts.background_color = "white"
  1080     opts.label_space = 5     # minimum number of pixels between axis labels
  1081 
  1082     try: lastDotplot(opts, args)
  1083     except KeyboardInterrupt: pass  # avoid silly error message
  1084     except Exception as e:
  1085         prog = os.path.basename(sys.argv[0])
  1086         sys.exit(prog + ": error: " + str(e))