scripts/last-dotplot
author Martin C. Frith
Fri Jul 31 14:48:36 2020 +0900 (21 months ago)
changeset 1075 70b0e512d696
parent 1074 170ab6c64728
child 1076 3b8d229f8359
permissions -rwxr-xr-x
last-dotplot: implementing annotation names...
     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 sizesPerText(texts, font, textDraw):
   397     sizes = 0, 0
   398     for t in texts:
   399         if textDraw is not None:
   400             sizes = textDraw.textsize(t, font=font)
   401         yield t, sizes
   402 
   403 def prettyNum(n):
   404     t = str(n)
   405     groups = []
   406     while t:
   407         groups.append(t[-3:])
   408         t = t[:-3]
   409     return ",".join(reversed(groups))
   410 
   411 def sizeText(size):
   412     suffixes = "bp", "kb", "Mb", "Gb"
   413     for i, x in enumerate(suffixes):
   414         j = 10 ** (i * 3)
   415         if size < j * 10:
   416             return "%.2g" % (1.0 * size / j) + x
   417         if size < j * 1000 or i == len(suffixes) - 1:
   418             return "%.0f" % (1.0 * size / j) + x
   419 
   420 def labelText(seqRange, labelOpt):
   421     seqName, beg, end, strandNum = seqRange
   422     if labelOpt == 1:
   423         return seqName + ": " + sizeText(end - beg)
   424     if labelOpt == 2:
   425         return seqName + ":" + prettyNum(beg) + ": " + sizeText(end - beg)
   426     if labelOpt == 3:
   427         return seqName + ":" + prettyNum(beg) + "-" + prettyNum(end)
   428     return seqName
   429 
   430 def rangeLabels(seqRanges, labelOpt, font, textDraw, textRot):
   431     x = y = 0
   432     for r in seqRanges:
   433         text = labelText(r, labelOpt)
   434         if textDraw is not None:
   435             x, y = textDraw.textsize(text, font=font)
   436             if textRot:
   437                 x, y = y, x
   438         yield text, x, y, r[3]
   439 
   440 def dataFromRanges(sortedRanges, font, textDraw, labelOpt, textRot):
   441     for seqName, rangeBeg, rangeEnd, strandNum in sortedRanges:
   442         out = [seqName, str(rangeBeg), str(rangeEnd)]
   443         if strandNum > 0:
   444             out.append(".+-"[strandNum])
   445         logging.info("\t".join(out))
   446     logging.info("")
   447     rangeSizes = [e - b for n, b, e, s in sortedRanges]
   448     labs = list(rangeLabels(sortedRanges, labelOpt, font, textDraw, textRot))
   449     margin = max(i[2] for i in labs)
   450     # xxx the margin may be too big, because some labels may get omitted
   451     return rangeSizes, labs, margin
   452 
   453 def div_ceil(x, y):
   454     '''Return x / y rounded up.'''
   455     q, r = divmod(x, y)
   456     return q + (r != 0)
   457 
   458 def get_bp_per_pix(rangeSizes, pixTweenRanges, maxPixels):
   459     '''Get the minimum bp-per-pixel that fits in the size limit.'''
   460     logging.info("choosing bp per pixel...")
   461     numOfRanges = len(rangeSizes)
   462     maxPixelsInRanges = maxPixels - pixTweenRanges * (numOfRanges - 1)
   463     if maxPixelsInRanges < numOfRanges:
   464         raise Exception("can't fit the image: too many sequences?")
   465     negLimit = -maxPixelsInRanges
   466     negBpPerPix = sum(rangeSizes) // negLimit
   467     while True:
   468         if sum(i // negBpPerPix for i in rangeSizes) >= negLimit:
   469             return -negBpPerPix
   470         negBpPerPix -= 1
   471 
   472 def getRangePixBegs(rangePixLens, pixTweenRanges, margin):
   473     '''Get the start pixel for each range.'''
   474     rangePixBegs = []
   475     pix_tot = margin - pixTweenRanges
   476     for i in rangePixLens:
   477         pix_tot += pixTweenRanges
   478         rangePixBegs.append(pix_tot)
   479         pix_tot += i
   480     return rangePixBegs
   481 
   482 def pixelData(rangeSizes, bp_per_pix, pixTweenRanges, margin):
   483     '''Return pixel information about the ranges.'''
   484     rangePixLens = [div_ceil(i, bp_per_pix) for i in rangeSizes]
   485     rangePixBegs = getRangePixBegs(rangePixLens, pixTweenRanges, margin)
   486     tot_pix = rangePixBegs[-1] + rangePixLens[-1]
   487     return rangePixBegs, rangePixLens, tot_pix
   488 
   489 def drawLineForward(hits, width, bp_per_pix, beg1, beg2, size):
   490     while True:
   491         q1, r1 = divmod(beg1, bp_per_pix)
   492         q2, r2 = divmod(beg2, bp_per_pix)
   493         hits[q2 * width + q1] |= 1
   494         next_pix = min(bp_per_pix - r1, bp_per_pix - r2)
   495         if next_pix >= size: break
   496         beg1 += next_pix
   497         beg2 += next_pix
   498         size -= next_pix
   499 
   500 def drawLineReverse(hits, width, bp_per_pix, beg1, beg2, size):
   501     while True:
   502         q1, r1 = divmod(beg1, bp_per_pix)
   503         q2, r2 = divmod(beg2, bp_per_pix)
   504         hits[q2 * width + q1] |= 2
   505         next_pix = min(bp_per_pix - r1, r2 + 1)
   506         if next_pix >= size: break
   507         beg1 += next_pix
   508         beg2 -= next_pix
   509         size -= next_pix
   510 
   511 def strandAndOrigin(ranges, beg, size):
   512     isReverseStrand = (beg < 0)
   513     if isReverseStrand:
   514         beg = -(beg + size)
   515     for rangeBeg, rangeEnd, isReverseRange, origin in ranges:
   516         if rangeEnd > beg:  # assumes the ranges are sorted
   517             return (isReverseStrand != isReverseRange), origin
   518 
   519 def alignmentPixels(width, height, alignments, bp_per_pix,
   520                     rangeDict1, rangeDict2):
   521     hits = [0] * (width * height)  # the image data
   522     for seq1, seq2, blocks in alignments:
   523         beg1, beg2, size = blocks[0]
   524         isReverse1, ori1 = strandAndOrigin(rangeDict1[seq1], beg1, size)
   525         isReverse2, ori2 = strandAndOrigin(rangeDict2[seq2], beg2, size)
   526         for beg1, beg2, size in blocks:
   527             if isReverse1:
   528                 beg1 = -(beg1 + size)
   529                 beg2 = -(beg2 + size)
   530             if isReverse1 == isReverse2:
   531                 drawLineForward(hits, width, bp_per_pix,
   532                                 ori1 + beg1, ori2 + beg2, size)
   533             else:
   534                 drawLineReverse(hits, width, bp_per_pix,
   535                                 ori1 + beg1, ori2 - beg2 - 1, size)
   536     return hits
   537 
   538 def orientedBlocks(alignments, seqIndex):
   539     otherIndex = 1 - seqIndex
   540     for a in alignments:
   541         seq1, seq2, blocks = a
   542         for b in blocks:
   543             beg1, beg2, size = b
   544             if b[seqIndex] < 0:
   545                 b = -(beg1 + size), -(beg2 + size), size
   546             yield a[seqIndex], b[seqIndex], a[otherIndex], b[otherIndex], size
   547 
   548 def drawJoins(im, alignments, bpPerPix, seqIndex, rangeDict1, rangeDict2):
   549     blocks = orientedBlocks(alignments, seqIndex)
   550     oldSeq1 = ""
   551     for seq1, beg1, seq2, beg2, size in sorted(blocks):
   552         isReverse1, ori1 = strandAndOrigin(rangeDict1[seq1], beg1, size)
   553         isReverse2, ori2 = strandAndOrigin(rangeDict2[seq2], beg2, size)
   554         end1 = beg1 + size - 1
   555         end2 = beg2 + size - 1
   556         if isReverse1:
   557             beg1 = -(beg1 + 1)
   558             end1 = -(end1 + 1)
   559         if isReverse2:
   560             beg2 = -(beg2 + 1)
   561             end2 = -(end2 + 1)
   562         newPix1 = (ori1 + beg1) // bpPerPix
   563         newPix2 = (ori2 + beg2) // bpPerPix
   564         if seq1 == oldSeq1:
   565             lowerPix2 = min(oldPix2, newPix2)
   566             upperPix2 = max(oldPix2, newPix2)
   567             midPix1 = (oldPix1 + newPix1) // 2
   568             if isReverse1:
   569                 midPix1 = (oldPix1 + newPix1 + 1) // 2
   570                 oldPix1, newPix1 = newPix1, oldPix1
   571             if upperPix2 - lowerPix2 > 1 and oldPix1 <= newPix1 <= oldPix1 + 1:
   572                 if seqIndex == 0:
   573                     box = midPix1, lowerPix2, midPix1 + 1, upperPix2 + 1
   574                 else:
   575                     box = lowerPix2, midPix1, upperPix2 + 1, midPix1 + 1
   576                 im.paste("lightgray", box)
   577         oldPix1 = (ori1 + end1) // bpPerPix
   578         oldPix2 = (ori2 + end2) // bpPerPix
   579         oldSeq1 = seq1
   580 
   581 def expandedSeqDict(seqDict):
   582     '''Allow lookup by short sequence names, e.g. chr7 as well as hg19.chr7.'''
   583     newDict = seqDict.copy()
   584     for name, x in seqDict.items():
   585         if "." in name:
   586             base = name.split(".")[-1]
   587             if base in newDict:  # an ambiguous case was found:
   588                 return seqDict   # so give up completely
   589             newDict[base] = x
   590     return newDict
   591 
   592 def readBed(fileName, rangeDict):
   593     for line in myOpen(fileName):
   594         w = line.split()
   595         if not w: continue
   596         seqName = w[0]
   597         if seqName not in rangeDict: continue
   598         seqRanges = rangeDict[seqName]
   599         beg = int(w[1])
   600         end = int(w[2])
   601         if all(beg >= i[2] or end <= i[1] for i in seqRanges):
   602             continue
   603         itemName = w[3] if len(w) > 3 and w[3] != "." else ""
   604         layer = 900
   605         color = "#fbf"
   606         if len(w) > 4:
   607             if w[4] != ".":
   608                 layer = float(w[4])
   609             if len(w) > 5:
   610                 if len(w) > 8 and w[8].count(",") == 2:
   611                     color = "rgb(" + w[8] + ")"
   612                 else:
   613                     strand = w[5]
   614                     isRev = (seqRanges[0][3] > 1)
   615                     if strand == "+" and not isRev or strand == "-" and isRev:
   616                         color = "#ffe8e8"
   617                     if strand == "-" and not isRev or strand == "+" and isRev:
   618                         color = "#e8e8ff"
   619         yield layer, color, seqName, beg, end, itemName
   620 
   621 def commaSeparatedInts(text):
   622     return map(int, text.rstrip(",").split(","))
   623 
   624 def readGenePred(opts, fileName, rangeDict):
   625     for line in myOpen(fileName):
   626         fields = line.split()  # xxx tab ???
   627         if not fields: continue
   628         geneName = fields[12 if len(fields) > 12 else 0]  # XXX ???
   629         if fields[2] not in "+-":
   630             fields = fields[1:]
   631         seqName = fields[1]
   632         if seqName not in rangeDict: continue
   633         seqRanges = rangeDict[seqName]
   634         #strand = fields[2]
   635         cdsBeg = int(fields[5])
   636         cdsEnd = int(fields[6])
   637         exonBegs = commaSeparatedInts(fields[8])
   638         exonEnds = commaSeparatedInts(fields[9])
   639         for beg, end in zip(exonBegs, exonEnds):
   640             if all(beg >= i[2] or end <= i[1] for i in seqRanges):
   641                 continue
   642             yield 300, opts.exon_color, seqName, beg, end, geneName
   643             b = max(beg, cdsBeg)
   644             e = min(end, cdsEnd)
   645             if b < e: yield 400, opts.cds_color, seqName, b, e, ""
   646 
   647 def readRmsk(fileName, rangeDict):
   648     for line in myOpen(fileName):
   649         fields = line.split()
   650         if len(fields) == 17:  # rmsk.txt
   651             seqName = fields[5]
   652             if seqName not in rangeDict: continue  # do this ASAP for speed
   653             beg = int(fields[6])
   654             end = int(fields[7])
   655             strand = fields[9]
   656             repeatName = fields[10]
   657             repeatClass = fields[11]
   658         elif len(fields) == 15:  # .out
   659             seqName = fields[4]
   660             if seqName not in rangeDict: continue
   661             beg = int(fields[5]) - 1
   662             end = int(fields[6])
   663             strand = fields[8]
   664             repeatName = fields[9]
   665             repeatClass = fields[10].split("/")[0]
   666         else:
   667             continue
   668         seqRanges = rangeDict[seqName]
   669         if all(beg >= i[2] or end <= i[1] for i in seqRanges):
   670             continue
   671         if repeatClass in ("Low_complexity", "Simple_repeat", "Satellite"):
   672             yield 200, "#fbf", seqName, beg, end, repeatName
   673         elif (strand == "+") != (seqRanges[0][3] > 1):
   674             yield 100, "#ffe8e8", seqName, beg, end, repeatName
   675         else:
   676             yield 100, "#e8e8ff", seqName, beg, end, repeatName
   677 
   678 def isExtraFirstGapField(fields):
   679     return fields[4].isdigit()
   680 
   681 def readGaps(opts, fileName, rangeDict):
   682     '''Read locations of unsequenced gaps, from an agp or gap file.'''
   683     for line in myOpen(fileName):
   684         w = line.split()
   685         if not w or w[0][0] == "#": continue
   686         if isExtraFirstGapField(w): w = w[1:]
   687         if w[4] not in "NU": continue
   688         seqName = w[0]
   689         if seqName not in rangeDict: continue
   690         end = int(w[2])
   691         beg = end - int(w[5])  # zero-based coordinate
   692         if w[7] == "yes":
   693             yield 3000, opts.bridged_color, seqName, beg, end, ""
   694         else:
   695             yield 2000, opts.unbridged_color, seqName, beg, end, ""
   696 
   697 def bedBoxes(beds, rangeDict, margin, edge, isTop, bpPerPix):
   698     for layer, color, seqName, bedBeg, bedEnd, name in beds:
   699         for rangeBeg, rangeEnd, isReverseRange, origin in rangeDict[seqName]:
   700             beg = max(bedBeg, rangeBeg)
   701             end = min(bedEnd, rangeEnd)
   702             if beg >= end: continue
   703             if isReverseRange:
   704                 beg, end = -end, -beg
   705             if layer <= 1000:
   706                 # include partly-covered pixels
   707                 pixBeg = (origin + beg) // bpPerPix
   708                 pixEnd = div_ceil(origin + end, bpPerPix)
   709             else:
   710                 # exclude partly-covered pixels
   711                 pixBeg = div_ceil(origin + beg, bpPerPix)
   712                 pixEnd = (origin + end) // bpPerPix
   713                 if pixEnd <= pixBeg: continue
   714                 if bedEnd >= rangeEnd:  # include partly-covered end pixels
   715                     if isReverseRange:
   716                         pixBeg = (origin + beg) // bpPerPix
   717                     else:
   718                         pixEnd = div_ceil(origin + end, bpPerPix)
   719             if isTop:
   720                 box = pixBeg, margin, pixEnd, edge
   721             else:
   722                 box = margin, pixBeg, edge, pixEnd
   723             yield layer, color, box
   724 
   725 def drawAnnotations(im, boxes):
   726     # xxx use partial transparency for different-color overlaps?
   727     for layer, color, box in boxes:
   728         im.paste(color, box)
   729 
   730 def placedLabels(labels, rangePixBegs, rangePixLens, beg, end):
   731     '''Return axis labels with endpoint & sort-order information.'''
   732     maxWidth = end - beg
   733     for i, j, k in zip(labels, rangePixBegs, rangePixLens):
   734         text, textWidth, textHeight, strandNum = i
   735         if textWidth > maxWidth:
   736             continue
   737         labelBeg = j + (k - textWidth) // 2
   738         labelEnd = labelBeg + textWidth
   739         sortKey = textWidth - k
   740         if labelBeg < beg:
   741             sortKey += maxWidth * (beg - labelBeg)
   742             labelBeg = beg
   743             labelEnd = beg + textWidth
   744         if labelEnd > end:
   745             sortKey += maxWidth * (labelEnd - end)
   746             labelEnd = end
   747             labelBeg = end - textWidth
   748         yield sortKey, labelBeg, labelEnd, text, textHeight, strandNum
   749 
   750 def nonoverlappingLabels(labels, minPixTweenLabels):
   751     '''Get a subset of non-overlapping axis labels, greedily.'''
   752     out = []
   753     for i in labels:
   754         beg = i[1] - minPixTweenLabels
   755         end = i[2] + minPixTweenLabels
   756         if all(j[2] <= beg or j[1] >= end for j in out):
   757             out.append(i)
   758     return out
   759 
   760 def axisImage(labels, rangePixBegs, rangePixLens, textRot,
   761               textAln, font, image_mode, opts):
   762     '''Make an image of axis labels.'''
   763     beg = rangePixBegs[0]
   764     end = rangePixBegs[-1] + rangePixLens[-1]
   765     margin = max(i[2] for i in labels)
   766     labels = sorted(placedLabels(labels, rangePixBegs, rangePixLens, beg, end))
   767     minPixTweenLabels = 0 if textRot else opts.label_space
   768     labels = nonoverlappingLabels(labels, minPixTweenLabels)
   769     image_size = (margin, end) if textRot else (end, margin)
   770     im = Image.new(image_mode, image_size, opts.margin_color)
   771     draw = ImageDraw.Draw(im)
   772     for sortKey, labelBeg, labelEnd, text, textHeight, strandNum in labels:
   773         base = margin - textHeight if textAln else 0
   774         position = (base, labelBeg) if textRot else (labelBeg, base)
   775         fill = ("black", opts.forwardcolor, opts.reversecolor)[strandNum]
   776         draw.text(position, text, font=font, fill=fill)
   777     return im
   778 
   779 def rangesPerSeq(sortedRanges):
   780     for seqName, group in itertools.groupby(sortedRanges, itemgetter(0)):
   781         yield seqName, sorted(group)
   782 
   783 def rangesWithOrigins(sortedRanges, rangePixBegs, rangePixLens, bpPerPix):
   784     for i, j, k in zip(sortedRanges, rangePixBegs, rangePixLens):
   785         seqName, rangeBeg, rangeEnd, strandNum = i
   786         isReverseRange = (strandNum > 1)
   787         if isReverseRange:
   788             origin = bpPerPix * (j + k) + rangeBeg
   789         else:
   790             origin = bpPerPix * j - rangeBeg
   791         yield seqName, (rangeBeg, rangeEnd, isReverseRange, origin)
   792 
   793 def rangesAndOriginsPerSeq(sortedRanges, rangePixBegs, rangePixLens, bpPerPix):
   794     a = rangesWithOrigins(sortedRanges, rangePixBegs, rangePixLens, bpPerPix)
   795     for seqName, group in itertools.groupby(a, itemgetter(0)):
   796         yield seqName, sorted(i[1] for i in group)
   797 
   798 def getFont(opts):
   799     if opts.fontfile:
   800         return ImageFont.truetype(opts.fontfile, opts.fontsize)
   801     fileNames = []
   802     try:
   803         x = ["fc-match", "-f%{file}", "arial"]
   804         p = subprocess.Popen(x, stdout=subprocess.PIPE, stderr=subprocess.PIPE,
   805                              universal_newlines=True)
   806         out, err = p.communicate()
   807         fileNames.append(out)
   808     except OSError as e:
   809         logging.info("fc-match error: " + str(e))
   810     fileNames.append("/Library/Fonts/Arial.ttf")  # for Mac
   811     for i in fileNames:
   812         try:
   813             font = ImageFont.truetype(i, opts.fontsize)
   814             logging.info("font: " + i)
   815             return font
   816         except IOError as e:
   817             logging.info("font load error: " + str(e))
   818     return ImageFont.load_default()
   819 
   820 def sequenceSizesAndNames(seqRanges):
   821     for seqName, ranges in itertools.groupby(seqRanges, itemgetter(0)):
   822         size = sum(e - b for n, b, e in ranges)
   823         yield size, seqName
   824 
   825 def biggestSequences(seqRanges, maxNumOfSequences):
   826     s = sorted(sequenceSizesAndNames(seqRanges), reverse=True)
   827     if len(s) > maxNumOfSequences:
   828         logging.warning("too many sequences - discarding the smallest ones")
   829         s = s[:maxNumOfSequences]
   830     return set(i[1] for i in s)
   831 
   832 def remainingSequenceRanges(seqRanges, alignments, seqIndex):
   833     remainingSequences = set(i[seqIndex] for i in alignments)
   834     return [i for i in seqRanges if i[0] in remainingSequences]
   835 
   836 def readAnnotations(opts, font, textDraw, sortedRanges,
   837                     bedFile, repFile, geneFile, gapFile):
   838     rangeDict = expandedSeqDict(dict(rangesPerSeq(sortedRanges)))
   839     annots = sorted(itertools.chain(readBed(bedFile, rangeDict),
   840                                     readRmsk(repFile, rangeDict),
   841                                     readGenePred(opts, geneFile, rangeDict),
   842                                     readGaps(opts, gapFile, rangeDict)))
   843     names = set(i[5] for i in annots)
   844     textSizes = dict(sizesPerText(names, font, textDraw))
   845     return annots, textSizes
   846 
   847 def lastDotplot(opts, args):
   848     logLevel = logging.INFO if opts.verbose else logging.WARNING
   849     logging.basicConfig(format="%(filename)s: %(message)s", level=logLevel)
   850 
   851     font = getFont(opts)
   852     image_mode = 'RGB'
   853     forward_color = ImageColor.getcolor(opts.forwardcolor, image_mode)
   854     reverse_color = ImageColor.getcolor(opts.reversecolor, image_mode)
   855     zipped_colors = zip(forward_color, reverse_color)
   856     overlap_color = tuple([(i + j) // 2 for i, j in zipped_colors])
   857 
   858     maxGap1, maxGapB1 = twoValuesFromOption(opts.max_gap1, ":")
   859     maxGap2, maxGapB2 = twoValuesFromOption(opts.max_gap2, ":")
   860 
   861     logging.info("reading alignments...")
   862     alnData = readAlignments(args[0], opts)
   863     alignments, seqRanges1, coverDict1, seqRanges2, coverDict2 = alnData
   864     if not alignments: raise Exception("there are no alignments")
   865     logging.info("cutting...")
   866     coverDict1 = dict(mergedRangesPerSeq(coverDict1))
   867     coverDict2 = dict(mergedRangesPerSeq(coverDict2))
   868     minAlignedBases = min(coveredLength(coverDict1), coveredLength(coverDict2))
   869     pad = int(opts.pad * minAlignedBases)
   870     cutRanges1 = list(trimmed(seqRanges1, coverDict1, minAlignedBases,
   871                               maxGap1, pad, pad))
   872     cutRanges2 = list(trimmed(seqRanges2, coverDict2, minAlignedBases,
   873                               maxGap2, pad, pad))
   874 
   875     biggestSeqs1 = biggestSequences(cutRanges1, opts.maxseqs)
   876     cutRanges1 = [i for i in cutRanges1 if i[0] in biggestSeqs1]
   877     alignments = [i for i in alignments if i[0] in biggestSeqs1]
   878     cutRanges2 = remainingSequenceRanges(cutRanges2, alignments, 1)
   879 
   880     biggestSeqs2 = biggestSequences(cutRanges2, opts.maxseqs)
   881     cutRanges2 = [i for i in cutRanges2 if i[0] in biggestSeqs2]
   882     alignments = [i for i in alignments if i[1] in biggestSeqs2]
   883     cutRanges1 = remainingSequenceRanges(cutRanges1, alignments, 0)
   884 
   885     logging.info("reading secondary alignments...")
   886     alnDataB = readSecondaryAlignments(opts, cutRanges1, cutRanges2)
   887     alignmentsB, seqRangesB1, coverDictB1, seqRangesB2, coverDictB2 = alnDataB
   888     logging.info("cutting...")
   889     coverDictB1 = dict(mergedRangesPerSeq(coverDictB1))
   890     coverDictB2 = dict(mergedRangesPerSeq(coverDictB2))
   891     cutRangesB1 = trimmed(seqRangesB1, coverDictB1, minAlignedBases,
   892                           maxGapB1, 0, 0)
   893     cutRangesB2 = trimmed(seqRangesB2, coverDictB2, minAlignedBases,
   894                           maxGapB2, 0, 0)
   895 
   896     logging.info("sorting...")
   897     sortOut = allSortedRanges(opts, alignments, alignmentsB,
   898                               cutRanges1, cutRangesB1, cutRanges2, cutRangesB2)
   899     sortedRanges1, sortedRanges2 = sortOut
   900 
   901     textDraw = None
   902     if opts.fontsize:
   903         textDraw = ImageDraw.Draw(Image.new(image_mode, (1, 1)))
   904 
   905     textRot1 = "vertical".startswith(opts.rot1)
   906     i1 = dataFromRanges(sortedRanges1, font, textDraw, opts.labels1, textRot1)
   907     rangeSizes1, labelData1, tMargin = i1
   908 
   909     textRot2 = "horizontal".startswith(opts.rot2)
   910     i2 = dataFromRanges(sortedRanges2, font, textDraw, opts.labels2, textRot2)
   911     rangeSizes2, labelData2, lMargin = i2
   912 
   913     logging.info("reading annotations...")
   914 
   915     a1 = readAnnotations(opts, font, textDraw, sortedRanges1,
   916                          opts.bed1, opts.rmsk1, opts.genePred1, opts.gap1)
   917     annots1, annoTextSizes1 = a1
   918 
   919     a2 = readAnnotations(opts, font, textDraw, sortedRanges2,
   920                          opts.bed2, opts.rmsk2, opts.genePred2, opts.gap2)
   921     annots2, annoTextSizes2 = a2
   922 
   923     bMargin = rMargin = 0  # xxx
   924 
   925     maxPixels1 = opts.width  - lMargin - rMargin
   926     maxPixels2 = opts.height - tMargin - bMargin
   927     bpPerPix1 = get_bp_per_pix(rangeSizes1, opts.border_pixels, maxPixels1)
   928     bpPerPix2 = get_bp_per_pix(rangeSizes2, opts.border_pixels, maxPixels2)
   929     bpPerPix = max(bpPerPix1, bpPerPix2)
   930     logging.info("bp per pixel = " + str(bpPerPix))
   931 
   932     p1 = pixelData(rangeSizes1, bpPerPix, opts.border_pixels, lMargin)
   933     rangePixBegs1, rangePixLens1, rMarginBeg = p1
   934     width = rMarginBeg + rMargin
   935     rangeDict1 = dict(rangesAndOriginsPerSeq(sortedRanges1, rangePixBegs1,
   936                                              rangePixLens1, bpPerPix))
   937 
   938     p2 = pixelData(rangeSizes2, bpPerPix, opts.border_pixels, tMargin)
   939     rangePixBegs2, rangePixLens2, bMarginBeg = p2
   940     height = bMarginBeg + bMargin
   941     rangeDict2 = dict(rangesAndOriginsPerSeq(sortedRanges2, rangePixBegs2,
   942                                              rangePixLens2, bpPerPix))
   943 
   944     logging.info("width:  " + str(width))
   945     logging.info("height: " + str(height))
   946 
   947     logging.info("processing alignments...")
   948     allAlignments = alignments + alignmentsB
   949     hits = alignmentPixels(width, height, allAlignments, bpPerPix,
   950                            rangeDict1, rangeDict2)
   951 
   952     rangeDict1 = expandedSeqDict(rangeDict1)
   953     rangeDict2 = expandedSeqDict(rangeDict2)
   954 
   955     boxes1 = bedBoxes(annots1, rangeDict1, tMargin, bMarginBeg, 1, bpPerPix)
   956     boxes2 = bedBoxes(annots2, rangeDict2, lMargin, rMarginBeg, 0, bpPerPix)
   957     boxes = sorted(itertools.chain(boxes1, boxes2))
   958 
   959     logging.info("drawing...")
   960 
   961     image_size = width, height
   962     im = Image.new(image_mode, image_size, opts.background_color)
   963 
   964     drawAnnotations(im, boxes)
   965 
   966     joinA, joinB = twoValuesFromOption(opts.join, ":")
   967     if joinA in "13":
   968         drawJoins(im, alignments, bpPerPix, 0, rangeDict1, rangeDict2)
   969     if joinB in "13":
   970         drawJoins(im, alignmentsB, bpPerPix, 0, rangeDict1, rangeDict2)
   971     if joinA in "23":
   972         drawJoins(im, alignments, bpPerPix, 1, rangeDict2, rangeDict1)
   973     if joinB in "23":
   974         drawJoins(im, alignmentsB, bpPerPix, 1, rangeDict2, rangeDict1)
   975 
   976     for i in range(height):
   977         for j in range(width):
   978             store_value = hits[i * width + j]
   979             xy = j, i
   980             if   store_value == 1: im.putpixel(xy, forward_color)
   981             elif store_value == 2: im.putpixel(xy, reverse_color)
   982             elif store_value == 3: im.putpixel(xy, overlap_color)
   983 
   984     if opts.fontsize != 0:
   985         axis1 = axisImage(labelData1, rangePixBegs1, rangePixLens1,
   986                           textRot1, False, font, image_mode, opts)
   987         if textRot1:
   988             axis1 = axis1.transpose(Image.ROTATE_90)
   989         axis2 = axisImage(labelData2, rangePixBegs2, rangePixLens2,
   990                           textRot2, textRot2, font, image_mode, opts)
   991         if not textRot2:
   992             axis2 = axis2.transpose(Image.ROTATE_270)
   993         im.paste(axis1, (0, 0))
   994         im.paste(axis2, (0, 0))
   995 
   996     for i in rangePixBegs1[1:]:
   997         box = i - opts.border_pixels, tMargin, i, bMarginBeg
   998         im.paste(opts.border_color, box)
   999 
  1000     for i in rangePixBegs2[1:]:
  1001         box = lMargin, i - opts.border_pixels, rMarginBeg, i
  1002         im.paste(opts.border_color, box)
  1003 
  1004     im.save(args[1])
  1005 
  1006 if __name__ == "__main__":
  1007     usage = """%prog --help
  1008    or: %prog [options] maf-or-tab-alignments dotplot.png
  1009    or: %prog [options] maf-or-tab-alignments dotplot.gif
  1010    or: ..."""
  1011     description = "Draw a dotplot of pair-wise sequence alignments in MAF or tabular format."
  1012     op = optparse.OptionParser(usage=usage, description=description)
  1013     op.add_option("-v", "--verbose", action="count",
  1014                   help="show progress messages & data about the plot")
  1015     # Replace "width" & "height" with a single "length" option?
  1016     op.add_option("-x", "--width", metavar="INT", type="int", default=1000,
  1017                   help="maximum width in pixels (default: %default)")
  1018     op.add_option("-y", "--height", metavar="INT", type="int", default=1000,
  1019                   help="maximum height in pixels (default: %default)")
  1020     op.add_option("-m", "--maxseqs", type="int", default=100, metavar="M",
  1021                   help="maximum number of horizontal or vertical sequences "
  1022                   "(default=%default)")
  1023     op.add_option("-1", "--seq1", metavar="PATTERN", action="append",
  1024                   default=[],
  1025                   help="which sequences to show from the 1st genome")
  1026     op.add_option("-2", "--seq2", metavar="PATTERN", action="append",
  1027                   default=[],
  1028                   help="which sequences to show from the 2nd genome")
  1029     op.add_option("-c", "--forwardcolor", metavar="COLOR", default="red",
  1030                   help="color for forward alignments (default: %default)")
  1031     op.add_option("-r", "--reversecolor", metavar="COLOR", default="blue",
  1032                   help="color for reverse alignments (default: %default)")
  1033     op.add_option("--alignments", metavar="FILE", help="secondary alignments")
  1034     op.add_option("--sort1", default="1", metavar="N",
  1035                   help="genome1 sequence order: 0=input order, 1=name order, "
  1036                   "2=length order, 3=alignment order (default=%default)")
  1037     op.add_option("--sort2", default="1", metavar="N",
  1038                   help="genome2 sequence order: 0=input order, 1=name order, "
  1039                   "2=length order, 3=alignment order (default=%default)")
  1040     op.add_option("--strands1", default="0", metavar="N", help=
  1041                   "genome1 sequence orientation: 0=forward orientation, "
  1042                   "1=alignment orientation (default=%default)")
  1043     op.add_option("--strands2", default="0", metavar="N", help=
  1044                   "genome2 sequence orientation: 0=forward orientation, "
  1045                   "1=alignment orientation (default=%default)")
  1046     op.add_option("--max-gap1", metavar="FRAC", default="0.5,2", help=
  1047                   "maximum unaligned (end,mid) gap in genome1: "
  1048                   "fraction of aligned length (default=%default)")
  1049     op.add_option("--max-gap2", metavar="FRAC", default="0.5,2", help=
  1050                   "maximum unaligned (end,mid) gap in genome2: "
  1051                   "fraction of aligned length (default=%default)")
  1052     op.add_option("--pad", metavar="FRAC", type="float", default=0.04, help=
  1053                   "pad length when cutting unaligned gaps: "
  1054                   "fraction of aligned length (default=%default)")
  1055     op.add_option("-j", "--join", default="0", metavar="N", help=
  1056                   "join: 0=nothing, 1=alignments adjacent in genome1, "
  1057                   "2=alignments adjacent in genome2 (default=%default)")
  1058     op.add_option("--border-pixels", metavar="INT", type="int", default=1,
  1059                   help="number of pixels between sequences (default=%default)")
  1060     op.add_option("--border-color", metavar="COLOR", default="black",
  1061                   help="color for pixels between sequences (default=%default)")
  1062     # --break-color and/or --break-pixels for intra-sequence breaks?
  1063     op.add_option("--margin-color", metavar="COLOR", default="#dcdcdc",
  1064                   help="margin color")
  1065 
  1066     og = optparse.OptionGroup(op, "Text options")
  1067     og.add_option("-f", "--fontfile", metavar="FILE",
  1068                   help="TrueType or OpenType font file")
  1069     og.add_option("-s", "--fontsize", metavar="SIZE", type="int", default=14,
  1070                   help="TrueType or OpenType font size (default: %default)")
  1071     og.add_option("--labels1", type="int", default=0, metavar="N", help=
  1072                   "genome1 labels: 0=name, 1=name:length, "
  1073                   "2=name:start:length, 3=name:start-end (default=%default)")
  1074     og.add_option("--labels2", type="int", default=0, metavar="N", help=
  1075                   "genome2 labels: 0=name, 1=name:length, "
  1076                   "2=name:start:length, 3=name:start-end (default=%default)")
  1077     og.add_option("--rot1", metavar="ROT", default="h",
  1078                   help="text rotation for the 1st genome (default=%default)")
  1079     og.add_option("--rot2", metavar="ROT", default="v",
  1080                   help="text rotation for the 2nd genome (default=%default)")
  1081     op.add_option_group(og)
  1082 
  1083     og = optparse.OptionGroup(op, "Annotation options")
  1084     og.add_option("--bed1", metavar="FILE",
  1085                   help="read genome1 annotations from BED file")
  1086     og.add_option("--bed2", metavar="FILE",
  1087                   help="read genome2 annotations from BED file")
  1088     og.add_option("--rmsk1", metavar="FILE", help="read genome1 repeats from "
  1089                   "RepeatMasker .out or rmsk.txt file")
  1090     og.add_option("--rmsk2", metavar="FILE", help="read genome2 repeats from "
  1091                   "RepeatMasker .out or rmsk.txt file")
  1092     op.add_option_group(og)
  1093 
  1094     og = optparse.OptionGroup(op, "Gene options")
  1095     og.add_option("--genePred1", metavar="FILE",
  1096                   help="read genome1 genes from genePred file")
  1097     og.add_option("--genePred2", metavar="FILE",
  1098                   help="read genome2 genes from genePred file")
  1099     og.add_option("--exon-color", metavar="COLOR", default="PaleGreen",
  1100                   help="color for exons (default=%default)")
  1101     og.add_option("--cds-color", metavar="COLOR", default="LimeGreen",
  1102                   help="color for protein-coding regions (default=%default)")
  1103     op.add_option_group(og)
  1104 
  1105     og = optparse.OptionGroup(op, "Unsequenced gap options")
  1106     og.add_option("--gap1", metavar="FILE",
  1107                   help="read genome1 unsequenced gaps from agp or gap file")
  1108     og.add_option("--gap2", metavar="FILE",
  1109                   help="read genome2 unsequenced gaps from agp or gap file")
  1110     og.add_option("--bridged-color", metavar="COLOR", default="yellow",
  1111                   help="color for bridged gaps (default: %default)")
  1112     og.add_option("--unbridged-color", metavar="COLOR", default="orange",
  1113                   help="color for unbridged gaps (default: %default)")
  1114     op.add_option_group(og)
  1115     (opts, args) = op.parse_args()
  1116     if len(args) != 2: op.error("2 arguments needed")
  1117 
  1118     opts.background_color = "white"
  1119     opts.label_space = 5     # minimum number of pixels between axis labels
  1120 
  1121     try: lastDotplot(opts, args)
  1122     except KeyboardInterrupt: pass  # avoid silly error message
  1123     except Exception as e:
  1124         prog = os.path.basename(sys.argv[0])
  1125         sys.exit(prog + ": error: " + str(e))