scripts/last-dotplot
author Martin C. Frith
Fri Jun 02 18:40:29 2017 +0900 (2017-06-02)
changeset 863 6a4915d5b5cb
parent 861 a75b439f0cf2
child 866 5182d8528ce9
permissions -rwxr-xr-x
last-dotplot: get bp-per-pixel faster
     1 #! /usr/bin/env python
     2 
     3 # Read pair-wise alignments in MAF or LAST tabular format: write an
     4 # "Oxford grid", a.k.a. dotplot.
     5 
     6 # TODO: Currently, pixels with zero aligned nt-pairs are white, and
     7 # pixels with one or more aligned nt-pairs are black.  This can look
     8 # too crowded for large genome alignments.  I tried shading each pixel
     9 # according to the number of aligned nt-pairs within it, but the
    10 # result is too faint.  How can this be done better?
    11 
    12 import fnmatch, itertools, optparse, os, re, sys
    13 
    14 # Try to make PIL/PILLOW work:
    15 try: from PIL import Image, ImageDraw, ImageFont, ImageColor
    16 except ImportError: import Image, ImageDraw, ImageFont, ImageColor
    17 
    18 def myOpen(fileName):  # faster than fileinput
    19     if fileName == "-":
    20         return sys.stdin
    21     return open(fileName)
    22 
    23 def warn(message):
    24     prog = os.path.basename(sys.argv[0])
    25     sys.stderr.write(prog + ": " + message + "\n")
    26 
    27 def croppedBlocks(blocks, range1, range2):
    28     cropBeg1, cropEnd1 = range1
    29     cropBeg2, cropEnd2 = range2
    30     if blocks[0][0] < 0: cropBeg1, cropEnd1 = -cropEnd1, -cropBeg1
    31     if blocks[0][1] < 0: cropBeg2, cropEnd2 = -cropEnd2, -cropBeg2
    32     for beg1, beg2, size in blocks:
    33         b1 = max(cropBeg1, beg1)
    34         e1 = min(cropEnd1, beg1 + size)
    35         if b1 >= e1: continue
    36         offset = beg2 - beg1
    37         b2 = max(cropBeg2, b1 + offset)
    38         e2 = min(cropEnd2, e1 + offset)
    39         if b2 >= e2: continue
    40         yield b2 - offset, b2, e2 - b2
    41 
    42 def tabBlocks(beg1, beg2, blocks):
    43     '''Get the gapless blocks of an alignment, from LAST tabular format.'''
    44     for i in blocks.split(","):
    45         if ":" in i:
    46             x, y = i.split(":")
    47             beg1 += int(x)
    48             beg2 += int(y)
    49         else:
    50             size = int(i)
    51             yield beg1, beg2, size
    52             beg1 += size
    53             beg2 += size
    54 
    55 def mafBlocks(beg1, beg2, seq1, seq2):
    56     '''Get the gapless blocks of an alignment, from MAF format.'''
    57     size = 0
    58     for x, y in itertools.izip(seq1, seq2):
    59         if x == "-":
    60             if size:
    61                 yield beg1, beg2, size
    62                 beg1 += size
    63                 beg2 += size
    64                 size = 0
    65             beg2 += 1
    66         elif y == "-":
    67             if size:
    68                 yield beg1, beg2, size
    69                 beg1 += size
    70                 beg2 += size
    71                 size = 0
    72             beg1 += 1
    73         else:
    74             size += 1
    75     if size: yield beg1, beg2, size
    76 
    77 def alignmentInput(lines):
    78     '''Get alignments and sequence lengths, from MAF or tabular format.'''
    79     mafCount = 0
    80     for line in lines:
    81         w = line.split()
    82         if line[0].isdigit():  # tabular format
    83             chr1, beg1, seqlen1 = w[1], int(w[2]), int(w[5])
    84             if w[4] == "-": beg1 -= seqlen1
    85             chr2, beg2, seqlen2 = w[6], int(w[7]), int(w[10])
    86             if w[9] == "-": beg2 -= seqlen2
    87             blocks = tabBlocks(beg1, beg2, w[11])
    88             yield chr1, seqlen1, chr2, seqlen2, blocks
    89         elif line[0] == "s":  # MAF format
    90             if mafCount == 0:
    91                 chr1, beg1, seqlen1, seq1 = w[1], int(w[2]), int(w[5]), w[6]
    92                 if w[4] == "-": beg1 -= seqlen1
    93                 mafCount = 1
    94             else:
    95                 chr2, beg2, seqlen2, seq2 = w[1], int(w[2]), int(w[5]), w[6]
    96                 if w[4] == "-": beg2 -= seqlen2
    97                 blocks = mafBlocks(beg1, beg2, seq1, seq2)
    98                 yield chr1, seqlen1, chr2, seqlen2, blocks
    99                 mafCount = 0
   100 
   101 def seqRangeFromText(text):
   102     if ":" in text:
   103         pattern, interval = text.rsplit(":", 1)
   104         if "-" in interval:
   105             beg, end = interval.rsplit("-", 1)
   106             return pattern, int(beg), int(end)  # beg may be negative
   107     return text, 0, sys.maxsize
   108 
   109 def rangeFromSeqName(seqRanges, name, seqLen):
   110     if not seqRanges: return 0, seqLen
   111     base = name.split(".")[-1]  # allow for names like hg19.chr7
   112     for pat, beg, end in seqRanges:
   113         if fnmatch.fnmatchcase(name, pat) or fnmatch.fnmatchcase(base, pat):
   114             return max(beg, 0), min(end, seqLen)
   115     return None
   116 
   117 def updateSeqs(isTrim, seqNames, seqLimits, seqName, seqRange, blocks, index):
   118     if seqName not in seqLimits:
   119         seqNames.append(seqName)
   120     if isTrim:
   121         beg = blocks[0][index]
   122         end = blocks[-1][index] + blocks[-1][2]
   123         if beg < 0: beg, end = -end, -beg
   124         if seqName in seqLimits:
   125             b, e = seqLimits[seqName]
   126             seqLimits[seqName] = min(b, beg), max(e, end)
   127         else:
   128             seqLimits[seqName] = beg, end
   129     else:
   130         seqLimits[seqName] = seqRange
   131 
   132 def readAlignments(fileName, opts):
   133     '''Get alignments and sequence limits, from MAF or tabular format.'''
   134     seqRanges1 = map(seqRangeFromText, opts.seq1)
   135     seqRanges2 = map(seqRangeFromText, opts.seq2)
   136 
   137     alignments = []
   138     seqNames1 = []
   139     seqNames2 = []
   140     seqLimits1 = {}
   141     seqLimits2 = {}
   142     lines = myOpen(fileName)
   143     for seqName1, seqLen1, seqName2, seqLen2, blocks in alignmentInput(lines):
   144         range1 = rangeFromSeqName(seqRanges1, seqName1, seqLen1)
   145         if not range1: continue
   146         range2 = rangeFromSeqName(seqRanges2, seqName2, seqLen2)
   147         if not range2: continue
   148         b = list(croppedBlocks(list(blocks), range1, range2))
   149         if not b: continue
   150         aln = seqName1, seqName2, b
   151         alignments.append(aln)
   152         updateSeqs(opts.trim1, seqNames1, seqLimits1, seqName1, range1, b, 0)
   153         updateSeqs(opts.trim2, seqNames2, seqLimits2, seqName2, range2, b, 1)
   154     return alignments, seqNames1, seqNames2, seqLimits1, seqLimits2
   155 
   156 def natural_sort_key(my_string):
   157     '''Return a sort key for "natural" ordering, e.g. chr9 < chr10.'''
   158     parts = re.split(r'(\d+)', my_string)
   159     parts[1::2] = map(int, parts[1::2])
   160     return parts
   161 
   162 def get_text_sizes(my_strings, font, fontsize, image_mode):
   163     '''Get widths & heights, in pixels, of some strings.'''
   164     if fontsize == 0: return [(0, 0) for i in my_strings]
   165     image_size = 1, 1
   166     im = Image.new(image_mode, image_size)
   167     draw = ImageDraw.Draw(im)
   168     return [draw.textsize(i, font=font) for i in my_strings]
   169 
   170 def sizeText(size):
   171     suffixes = "bp", "kb", "Mb", "Gb"
   172     for i, x in enumerate(suffixes):
   173         j = 10 ** (i * 3)
   174         if size < j * 10:
   175             return "%.2g" % (1.0 * size / j) + x
   176         if size < j * 1000 or i == len(suffixes) - 1:
   177             return "%.0f" % (1.0 * size / j) + x
   178 
   179 def seqNameAndSizeText(seqName, seqSize):
   180     return seqName + ": " + sizeText(seqSize)
   181 
   182 def getSeqInfo(sortOpt, seqNames, seqLimits,
   183                font, fontsize, image_mode, isShowSize):
   184     '''Return miscellaneous information about the sequences.'''
   185     if sortOpt == 1:
   186         seqNames.sort(key=natural_sort_key)
   187     seqSizes = [seqLimits[i][1] - seqLimits[i][0] for i in seqNames]
   188     if sortOpt == 2:
   189         seqRecords = sorted(zip(seqSizes, seqNames), reverse=True)
   190         seqSizes = [i[0] for i in seqRecords]
   191         seqNames = [i[1] for i in seqRecords]
   192     if isShowSize:
   193         seqLabels = map(seqNameAndSizeText, seqNames, seqSizes)
   194     else:
   195         seqLabels = seqNames
   196     labelSizes = get_text_sizes(seqLabels, font, fontsize, image_mode)
   197     margin = max(zip(*labelSizes)[1])  # maximum text height
   198     return seqNames, seqSizes, seqLabels, labelSizes, margin
   199 
   200 def div_ceil(x, y):
   201     '''Return x / y rounded up.'''
   202     q, r = divmod(x, y)
   203     return q + (r != 0)
   204 
   205 def get_bp_per_pix(seq_sizes, pix_tween_seqs, pix_limit):
   206     '''Get the minimum bp-per-pixel that fits in the size limit.'''
   207     seq_num = len(seq_sizes)
   208     seq_pix_limit = pix_limit - pix_tween_seqs * (seq_num - 1)
   209     if seq_pix_limit < seq_num:
   210         raise Exception("can't fit the image: too many sequences?")
   211     negLimit = -seq_pix_limit
   212     negBpPerPix = sum(seq_sizes) // negLimit
   213     while True:
   214         if sum(i // negBpPerPix for i in seq_sizes) >= negLimit:
   215             return -negBpPerPix
   216         negBpPerPix -= 1
   217 
   218 def get_seq_starts(seq_pix, pix_tween_seqs, margin):
   219     '''Get the start pixel for each sequence.'''
   220     seq_starts = []
   221     pix_tot = margin - pix_tween_seqs
   222     for i in seq_pix:
   223         pix_tot += pix_tween_seqs
   224         seq_starts.append(pix_tot)
   225         pix_tot += i
   226     return seq_starts
   227 
   228 def get_pix_info(seq_sizes, bp_per_pix, pix_tween_seqs, margin):
   229     '''Return pixel information about the sequences.'''
   230     seq_pix = [div_ceil(i, bp_per_pix) for i in seq_sizes]
   231     seq_starts = get_seq_starts(seq_pix, pix_tween_seqs, margin)
   232     tot_pix = seq_starts[-1] + seq_pix[-1]
   233     return seq_pix, seq_starts, tot_pix
   234 
   235 def drawLineForward(hits, width, bp_per_pix, beg1, beg2, size):
   236     while True:
   237         q1, r1 = divmod(beg1, bp_per_pix)
   238         q2, r2 = divmod(beg2, bp_per_pix)
   239         hits[q2 * width + q1] |= 1
   240         next_pix = min(bp_per_pix - r1, bp_per_pix - r2)
   241         if next_pix >= size: break
   242         beg1 += next_pix
   243         beg2 += next_pix
   244         size -= next_pix
   245 
   246 def drawLineReverse(hits, width, bp_per_pix, beg1, beg2, size):
   247     beg2 = -1 - beg2
   248     while True:
   249         q1, r1 = divmod(beg1, bp_per_pix)
   250         q2, r2 = divmod(beg2, bp_per_pix)
   251         hits[q2 * width + q1] |= 2
   252         next_pix = min(bp_per_pix - r1, r2 + 1)
   253         if next_pix >= size: break
   254         beg1 += next_pix
   255         beg2 -= next_pix
   256         size -= next_pix
   257 
   258 def alignmentPixels(width, height, alignments, bp_per_pix, origins1, origins2):
   259     hits = [0] * (width * height)  # the image data
   260     for seq1, seq2, blocks in alignments:
   261         ori1 = origins1[seq1]
   262         ori2 = origins2[seq2]
   263         for beg1, beg2, size in blocks:
   264             if beg1 < 0:
   265                 beg1 = -(beg1 + size)
   266                 beg2 = -(beg2 + size)
   267             if beg2 >= 0:
   268                 drawLineForward(hits, width, bp_per_pix,
   269                                 beg1 + ori1, beg2 + ori2, size)
   270             else:
   271                 drawLineReverse(hits, width, bp_per_pix,
   272                                 beg1 + ori1, beg2 - ori2, size)
   273     return hits
   274 
   275 def expandedSeqDict(seqDict):
   276     '''Allow lookup by short sequence names, e.g. chr7 as well as hg19.chr7.'''
   277     newDict = seqDict.copy()
   278     for name, x in seqDict.items():
   279         if "." in name:
   280             base = name.split(".")[-1]
   281             if base in newDict:  # an ambiguous case was found:
   282                 return seqDict   # so give up completely
   283             newDict[base] = x
   284     return newDict
   285 
   286 def readBed(fileName, seqLimits):
   287     if not fileName: return
   288     for line in myOpen(fileName):
   289         w = line.split()
   290         if not w: continue
   291         seqName = w[0]
   292         if seqName not in seqLimits: continue
   293         beg = int(w[1])
   294         end = int(w[2])
   295         layer = 900
   296         color = "#ffe4ff"
   297         if len(w) > 4:
   298             if w[4] != ".":
   299                 layer = float(w[4])
   300             if len(w) > 5:
   301                 if len(w) > 8 and w[8].count(",") == 2:
   302                     color = "rgb(" + w[8] + ")"
   303                 elif w[5] == "+":
   304                     color = "#fff4f4"
   305                 elif w[5] == "-":
   306                     color = "#f4f4ff"
   307         yield layer, color, seqName, beg, end
   308 
   309 def commaSeparatedInts(text):
   310     return map(int, text.rstrip(",").split(","))
   311 
   312 def readGenePred(opts, fileName, seqLimits):
   313     if not fileName: return
   314     for line in myOpen(fileName):
   315         fields = line.split()
   316         if not fields: continue
   317         if fields[2] not in "+-": fields = fields[1:]
   318         seqName = fields[1]
   319         if seqName not in seqLimits: continue
   320         #strand = fields[2]
   321         cdsBeg = int(fields[5])
   322         cdsEnd = int(fields[6])
   323         exonBegs = commaSeparatedInts(fields[8])
   324         exonEnds = commaSeparatedInts(fields[9])
   325         for beg, end in zip(exonBegs, exonEnds):
   326             yield 300, opts.exon_color, seqName, beg, end
   327             b = max(beg, cdsBeg)
   328             e = min(end, cdsEnd)
   329             if b < e: yield 400, opts.cds_color, seqName, b, e
   330 
   331 def readRmsk(fileName, seqLimits):
   332     if not fileName: return
   333     for line in myOpen(fileName):
   334         fields = line.split()
   335         if len(fields) == 17:  # rmsk.txt
   336             seqName = fields[5]
   337             if seqName not in seqLimits: continue  # do this ASAP for speed
   338             beg = int(fields[6])
   339             end = int(fields[7])
   340             strand = fields[9]
   341             repeatClass = fields[11]
   342         elif len(fields) == 15:  # .out
   343             seqName = fields[4]
   344             if seqName not in seqLimits: continue
   345             beg = int(fields[5]) - 1
   346             end = int(fields[6])
   347             strand = fields[8]
   348             repeatClass = fields[10]
   349         else:
   350             continue
   351         if repeatClass in ("Low_complexity", "Simple_repeat"):
   352             yield 200, "#ffe4ff", seqName, beg, end
   353         elif strand == "+":
   354             yield 100, "#fff4f4", seqName, beg, end
   355         else:
   356             yield 100, "#f4f4ff", seqName, beg, end
   357 
   358 def isExtraFirstGapField(fields):
   359     return fields[4].isdigit()
   360 
   361 def readGaps(opts, fileName, seqLimits):
   362     '''Read locations of unsequenced gaps, from an agp or gap file.'''
   363     if not fileName: return
   364     for line in myOpen(fileName):
   365         w = line.split()
   366         if not w or w[0][0] == "#": continue
   367         if isExtraFirstGapField(w): w = w[1:]
   368         if w[4] not in "NU": continue
   369         seqName = w[0]
   370         if seqName not in seqLimits: continue
   371         end = int(w[2])
   372         beg = end - int(w[5])  # zero-based coordinate
   373         if w[7] == "yes":
   374             yield 3000, opts.bridged_color, seqName, beg, end
   375         else:
   376             yield 2000, opts.unbridged_color, seqName, beg, end
   377 
   378 def bedBoxes(beds, seqLimits, origins, margin, edge, isTop, bpPerPix):
   379     for layer, color, seqName, beg, end in beds:
   380         cropBeg, cropEnd = seqLimits[seqName]
   381         beg = max(beg, cropBeg)
   382         end = min(end, cropEnd)
   383         if beg >= end: continue
   384         ori = origins[seqName]
   385         if layer <= 1000:
   386             # include partly-covered pixels
   387             b = (ori + beg) // bpPerPix
   388             e = div_ceil(ori + end, bpPerPix)
   389         else:
   390             # exclude partly-covered pixels
   391             b = div_ceil(ori + beg, bpPerPix)
   392             e = (ori + end) // bpPerPix
   393             if e <= b: continue
   394         if isTop:
   395             box = b, margin, e, edge
   396         else:
   397             box = margin, b, edge, e
   398         yield layer, color, box
   399 
   400 def drawAnnotations(im, boxes):
   401     # xxx use partial transparency for different-color overlaps?
   402     for layer, color, box in boxes:
   403         im.paste(color, box)
   404 
   405 def make_label(text, text_size, range_start, range_size):
   406     '''Return an axis label with endpoint & sort-order information.'''
   407     text_width  = text_size[0]
   408     label_start = range_start + (range_size - text_width) // 2
   409     label_end   = label_start + text_width
   410     sort_key    = text_width - range_size
   411     return sort_key, label_start, label_end, text
   412 
   413 def get_nonoverlapping_labels(labels, label_space):
   414     '''Get a subset of non-overlapping axis labels, greedily.'''
   415     nonoverlapping_labels = []
   416     for i in labels:
   417         if True not in [i[1] < j[2] + label_space and j[1] < i[2] + label_space
   418                         for j in nonoverlapping_labels]:
   419             nonoverlapping_labels.append(i)
   420     return nonoverlapping_labels
   421 
   422 def get_axis_image(seqNames, name_sizes, seq_starts, seq_pix,
   423                    font, image_mode, opts):
   424     '''Make an image of axis labels.'''
   425     min_pos = seq_starts[0]
   426     max_pos = seq_starts[-1] + seq_pix[-1]
   427     height = max(zip(*name_sizes)[1])
   428     labels = map(make_label, seqNames, name_sizes, seq_starts, seq_pix)
   429     labels = [i for i in labels if i[1] >= min_pos and i[2] <= max_pos]
   430     labels.sort()
   431     labels = get_nonoverlapping_labels(labels, opts.label_space)
   432     image_size = max_pos, height
   433     im = Image.new(image_mode, image_size, opts.border_color)
   434     draw = ImageDraw.Draw(im)
   435     for i in labels:
   436         position = i[1], 0
   437         draw.text(position, i[3], font=font, fill=opts.text_color)
   438     return im
   439 
   440 def seqOrigins(seqNames, seq_starts, seqLimits, bp_per_pix):
   441     for i, j in zip(seqNames, seq_starts):
   442         yield i, bp_per_pix * j - seqLimits[i][0]
   443 
   444 def lastDotplot(opts, args):
   445     if opts.fontfile:  font = ImageFont.truetype(opts.fontfile, opts.fontsize)
   446     else:              font = ImageFont.load_default()
   447 
   448     image_mode = 'RGB'
   449     forward_color = ImageColor.getcolor(opts.forwardcolor, image_mode)
   450     reverse_color = ImageColor.getcolor(opts.reversecolor, image_mode)
   451     zipped_colors = zip(forward_color, reverse_color)
   452     overlap_color = tuple([(i + j) // 2 for i, j in zipped_colors])
   453 
   454     warn("reading alignments...")
   455     alignmentInfo = readAlignments(args[0], opts)
   456     alignments, seqNames1, seqNames2, seqLimits1, seqLimits2 = alignmentInfo
   457     warn("done")
   458     if not alignments: raise Exception("there are no alignments")
   459 
   460     i1 = getSeqInfo(opts.sort1, seqNames1, seqLimits1,
   461                     font, opts.fontsize, image_mode, opts.lengths1)
   462     seqNames1, seqSizes1, seqLabels1, labelSizes1, margin1 = i1
   463 
   464     i2 = getSeqInfo(opts.sort2, seqNames2, seqLimits2,
   465                     font, opts.fontsize, image_mode, opts.lengths2)
   466     seqNames2, seqSizes2, seqLabels2, labelSizes2, margin2 = i2
   467 
   468     warn("choosing bp per pixel...")
   469     pix_limit1 = opts.width  - margin1
   470     pix_limit2 = opts.height - margin2
   471     bpPerPix1 = get_bp_per_pix(seqSizes1, opts.border_pixels, pix_limit1)
   472     bpPerPix2 = get_bp_per_pix(seqSizes2, opts.border_pixels, pix_limit2)
   473     bpPerPix = max(bpPerPix1, bpPerPix2)
   474     warn("bp per pixel = " + str(bpPerPix))
   475 
   476     seq_pix1, seq_starts1, width  = get_pix_info(seqSizes1, bpPerPix,
   477                                                  opts.border_pixels, margin1)
   478     seq_pix2, seq_starts2, height = get_pix_info(seqSizes2, bpPerPix,
   479                                                  opts.border_pixels, margin2)
   480     warn("width:  " + str(width))
   481     warn("height: " + str(height))
   482 
   483     origins1 = dict(seqOrigins(seqNames1, seq_starts1, seqLimits1, bpPerPix))
   484     origins2 = dict(seqOrigins(seqNames2, seq_starts2, seqLimits2, bpPerPix))
   485 
   486     warn("processing alignments...")
   487     hits = alignmentPixels(width, height, alignments, bpPerPix,
   488                            origins1, origins2)
   489     warn("done")
   490 
   491     image_size = width, height
   492     im = Image.new(image_mode, image_size, opts.background_color)
   493 
   494     seqLimits1 = expandedSeqDict(seqLimits1)
   495     seqLimits2 = expandedSeqDict(seqLimits2)
   496     origins1 = expandedSeqDict(origins1)
   497     origins2 = expandedSeqDict(origins2)
   498 
   499     beds1 = itertools.chain(readBed(opts.bed1, seqLimits1),
   500                             readRmsk(opts.rmsk1, seqLimits1),
   501                             readGenePred(opts, opts.genePred1, seqLimits1),
   502                             readGaps(opts, opts.gap1, seqLimits1))
   503     b1 = bedBoxes(beds1, seqLimits1, origins1, margin2, height, True, bpPerPix)
   504 
   505     beds2 = itertools.chain(readBed(opts.bed2, seqLimits2),
   506                             readRmsk(opts.rmsk2, seqLimits2),
   507                             readGenePred(opts, opts.genePred2, seqLimits2),
   508                             readGaps(opts, opts.gap2, seqLimits2))
   509     b2 = bedBoxes(beds2, seqLimits2, origins2, margin1, width, False, bpPerPix)
   510 
   511     boxes = sorted(itertools.chain(b1, b2))
   512     drawAnnotations(im, boxes)
   513 
   514     for i in range(height):
   515         for j in range(width):
   516             store_value = hits[i * width + j]
   517             xy = j, i
   518             if   store_value == 1: im.putpixel(xy, forward_color)
   519             elif store_value == 2: im.putpixel(xy, reverse_color)
   520             elif store_value == 3: im.putpixel(xy, overlap_color)
   521 
   522     if opts.fontsize != 0:
   523         axis1 = get_axis_image(seqLabels1, labelSizes1, seq_starts1, seq_pix1,
   524                                font, image_mode, opts)
   525         axis2 = get_axis_image(seqLabels2, labelSizes2, seq_starts2, seq_pix2,
   526                                font, image_mode, opts)
   527         axis2 = axis2.transpose(Image.ROTATE_270)  # !!! bug hotspot
   528         im.paste(axis1, (0, 0))
   529         im.paste(axis2, (0, 0))
   530 
   531     for i in seq_starts1[1:]:
   532         box = i - opts.border_pixels, margin2, i, height
   533         im.paste(opts.border_color, box)
   534 
   535     for i in seq_starts2[1:]:
   536         box = margin1, i - opts.border_pixels, width, i
   537         im.paste(opts.border_color, box)
   538 
   539     im.save(args[1])
   540 
   541 if __name__ == "__main__":
   542     usage = """%prog --help
   543    or: %prog [options] maf-or-tab-alignments dotplot.png
   544    or: %prog [options] maf-or-tab-alignments dotplot.gif
   545    or: ..."""
   546     description = "Draw a dotplot of pair-wise sequence alignments in MAF or tabular format."
   547     op = optparse.OptionParser(usage=usage, description=description)
   548     op.add_option("-1", "--seq1", metavar="PATTERN", action="append",
   549                   default=[],
   550                   help="which sequences to show from the 1st genome")
   551     op.add_option("-2", "--seq2", metavar="PATTERN", action="append",
   552                   default=[],
   553                   help="which sequences to show from the 2nd genome")
   554     # Replace "width" & "height" with a single "length" option?
   555     op.add_option("-x", "--width", type="int", default=1000,
   556                   help="maximum width in pixels (default: %default)")
   557     op.add_option("-y", "--height", type="int", default=1000,
   558                   help="maximum height in pixels (default: %default)")
   559     op.add_option("-c", "--forwardcolor", metavar="COLOR", default="red",
   560                   help="color for forward alignments (default: %default)")
   561     op.add_option("-r", "--reversecolor", metavar="COLOR", default="blue",
   562                   help="color for reverse alignments (default: %default)")
   563     op.add_option("--sort1", type="int", default=1, metavar="N",
   564                   help="genome1 sequence order: 0=input order, 1=name order, "
   565                   "2=length order (default=%default)")
   566     op.add_option("--sort2", type="int", default=1, metavar="N",
   567                   help="genome2 sequence order: 0=input order, 1=name order, "
   568                   "2=length order (default=%default)")
   569     op.add_option("--trim1", action="store_true",
   570                   help="trim unaligned sequence flanks from the 1st genome")
   571     op.add_option("--trim2", action="store_true",
   572                   help="trim unaligned sequence flanks from the 2nd genome")
   573     op.add_option("--border-pixels", metavar="INT", type="int", default=1,
   574                   help="number of pixels between sequences (default=%default)")
   575     op.add_option("--border-color", metavar="COLOR", default="#dcdcdc",
   576                   help="color for pixels between sequences (default=%default)")
   577     # xxx --margin-color?
   578 
   579     og = optparse.OptionGroup(op, "Text options")
   580     og.add_option("-f", "--fontfile", metavar="FILE",
   581                   help="TrueType or OpenType font file")
   582     og.add_option("-s", "--fontsize", metavar="SIZE", type="int", default=11,
   583                   help="TrueType or OpenType font size (default: %default)")
   584     og.add_option("--lengths1", action="store_true",
   585                   help="show sequence lengths for the 1st (horizontal) genome")
   586     og.add_option("--lengths2", action="store_true",
   587                   help="show sequence lengths for the 2nd (vertical) genome")
   588     op.add_option_group(og)
   589 
   590     og = optparse.OptionGroup(op, "Annotation options")
   591     og.add_option("--bed1", metavar="FILE",
   592                   help="read genome1 annotations from BED file")
   593     og.add_option("--bed2", metavar="FILE",
   594                   help="read genome2 annotations from BED file")
   595     og.add_option("--rmsk1", metavar="FILE", help="read genome1 repeats from "
   596                   "RepeatMasker .out or rmsk.txt file")
   597     og.add_option("--rmsk2", metavar="FILE", help="read genome2 repeats from "
   598                   "RepeatMasker .out or rmsk.txt file")
   599     op.add_option_group(og)
   600 
   601     og = optparse.OptionGroup(op, "Gene options")
   602     og.add_option("--genePred1", metavar="FILE",
   603                   help="read genome1 genes from genePred file")
   604     og.add_option("--genePred2", metavar="FILE",
   605                   help="read genome2 genes from genePred file")
   606     og.add_option("--exon-color", metavar="COLOR", default="#dfd",
   607                   help="color for exons (default=%default)")
   608     og.add_option("--cds-color", metavar="COLOR", default="#bdb",
   609                   help="color for protein-coding regions (default=%default)")
   610     op.add_option_group(og)
   611 
   612     og = optparse.OptionGroup(op, "Unsequenced gap options")
   613     og.add_option("--gap1", metavar="FILE",
   614                   help="read genome1 unsequenced gaps from agp or gap file")
   615     og.add_option("--gap2", metavar="FILE",
   616                   help="read genome2 unsequenced gaps from agp or gap file")
   617     og.add_option("--bridged-color", metavar="COLOR", default="yellow",
   618                   help="color for bridged gaps (default: %default)")
   619     og.add_option("--unbridged-color", metavar="COLOR", default="pink",
   620                   help="color for unbridged gaps (default: %default)")
   621     op.add_option_group(og)
   622     (opts, args) = op.parse_args()
   623     if len(args) != 2: op.error("2 arguments needed")
   624 
   625     opts.text_color = "black"
   626     opts.background_color = "white"
   627     opts.label_space = 5     # minimum number of pixels between axis labels
   628 
   629     try: lastDotplot(opts, args)
   630     except KeyboardInterrupt: pass  # avoid silly error message
   631     except Exception, e:
   632         prog = os.path.basename(sys.argv[0])
   633         sys.exit(prog + ": error: " + str(e))