scripts/last-dotplot
author Martin C. Frith
Thu May 18 14:23:58 2017 +0900 (2017-05-18)
changeset 860 6e8ff424ce2b
parent 859 1ecdbf2ddb78
child 861 a75b439f0cf2
permissions -rwxr-xr-x
last-dotplot: add genePred and rmsk options
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#! /usr/bin/env python
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# Read pair-wise alignments in MAF or LAST tabular format: write an
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# "Oxford grid", a.k.a. dotplot.
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# TODO: Currently, pixels with zero aligned nt-pairs are white, and
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# pixels with one or more aligned nt-pairs are black.  This can look
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# too crowded for large genome alignments.  I tried shading each pixel
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# according to the number of aligned nt-pairs within it, but the
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# result is too faint.  How can this be done better?
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import fnmatch, itertools, optparse, os, re, sys
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# Try to make PIL/PILLOW work:
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try: from PIL import Image, ImageDraw, ImageFont, ImageColor
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except ImportError: import Image, ImageDraw, ImageFont, ImageColor
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def myOpen(fileName):  # faster than fileinput
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    if fileName == "-":
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        return sys.stdin
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    return open(fileName)
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def warn(message):
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    prog = os.path.basename(sys.argv[0])
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    sys.stderr.write(prog + ": " + message + "\n")
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def croppedBlocks(blocks, range1, range2):
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    cropBeg1, cropEnd1 = range1
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    cropBeg2, cropEnd2 = range2
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    if blocks[0][0] < 0: cropBeg1, cropEnd1 = -cropEnd1, -cropBeg1
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    if blocks[0][1] < 0: cropBeg2, cropEnd2 = -cropEnd2, -cropBeg2
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    for beg1, beg2, size in blocks:
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        b1 = max(cropBeg1, beg1)
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        e1 = min(cropEnd1, beg1 + size)
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        if b1 >= e1: continue
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        offset = beg2 - beg1
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        b2 = max(cropBeg2, b1 + offset)
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        e2 = min(cropEnd2, e1 + offset)
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        if b2 >= e2: continue
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        yield b2 - offset, b2, e2 - b2
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def tabBlocks(beg1, beg2, blocks):
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    '''Get the gapless blocks of an alignment, from LAST tabular format.'''
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    for i in blocks.split(","):
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        if ":" in i:
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            x, y = i.split(":")
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            beg1 += int(x)
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            beg2 += int(y)
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        else:
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            size = int(i)
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            yield beg1, beg2, size
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            beg1 += size
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            beg2 += size
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def mafBlocks(beg1, beg2, seq1, seq2):
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    '''Get the gapless blocks of an alignment, from MAF format.'''
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    size = 0
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    for x, y in itertools.izip(seq1, seq2):
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        if x == "-":
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            if size:
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                yield beg1, beg2, size
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                beg1 += size
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                beg2 += size
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                size = 0
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            beg2 += 1
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        elif y == "-":
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            if size:
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                yield beg1, beg2, size
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                beg1 += size
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                beg2 += size
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                size = 0
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            beg1 += 1
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        else:
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            size += 1
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    if size: yield beg1, beg2, size
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def alignmentInput(lines):
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    '''Get alignments and sequence lengths, from MAF or tabular format.'''
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    mafCount = 0
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    for line in lines:
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        w = line.split()
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        if line[0].isdigit():  # tabular format
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            chr1, beg1, seqlen1 = w[1], int(w[2]), int(w[5])
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            if w[4] == "-": beg1 -= seqlen1
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            chr2, beg2, seqlen2 = w[6], int(w[7]), int(w[10])
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            if w[9] == "-": beg2 -= seqlen2
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            blocks = tabBlocks(beg1, beg2, w[11])
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            yield chr1, seqlen1, chr2, seqlen2, blocks
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        elif line[0] == "s":  # MAF format
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            if mafCount == 0:
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                chr1, beg1, seqlen1, seq1 = w[1], int(w[2]), int(w[5]), w[6]
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                if w[4] == "-": beg1 -= seqlen1
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                mafCount = 1
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            else:
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                chr2, beg2, seqlen2, seq2 = w[1], int(w[2]), int(w[5]), w[6]
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                if w[4] == "-": beg2 -= seqlen2
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                blocks = mafBlocks(beg1, beg2, seq1, seq2)
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                yield chr1, seqlen1, chr2, seqlen2, blocks
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                mafCount = 0
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def seqRangeFromText(text):
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    if ":" in text:
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        pattern, interval = text.rsplit(":", 1)
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        if "-" in interval:
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            beg, end = interval.rsplit("-", 1)
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            return pattern, int(beg), int(end)  # beg may be negative
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    return text, 0, sys.maxsize
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def rangeFromSeqName(seqRanges, name, seqLen):
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    if not seqRanges: return 0, seqLen
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    base = name.split(".")[-1]  # allow for names like hg19.chr7
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    for pat, beg, end in seqRanges:
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        if fnmatch.fnmatchcase(name, pat) or fnmatch.fnmatchcase(base, pat):
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            return max(beg, 0), min(end, seqLen)
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    return None
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def updateSeqs(isTrim, seqNames, seqLimits, seqName, seqRange, blocks, index):
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    if seqName not in seqLimits:
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        seqNames.append(seqName)
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    if isTrim:
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        beg = blocks[0][index]
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        end = blocks[-1][index] + blocks[-1][2]
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        if beg < 0: beg, end = -end, -beg
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        if seqName in seqLimits:
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            b, e = seqLimits[seqName]
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            seqLimits[seqName] = min(b, beg), max(e, end)
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        else:
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            seqLimits[seqName] = beg, end
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    else:
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        seqLimits[seqName] = seqRange
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def readAlignments(fileName, opts):
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    '''Get alignments and sequence limits, from MAF or tabular format.'''
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    seqRanges1 = map(seqRangeFromText, opts.seq1)
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    seqRanges2 = map(seqRangeFromText, opts.seq2)
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    alignments = []
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    seqNames1 = []
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    seqNames2 = []
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    seqLimits1 = {}
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    seqLimits2 = {}
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    lines = myOpen(fileName)
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    for seqName1, seqLen1, seqName2, seqLen2, blocks in alignmentInput(lines):
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        range1 = rangeFromSeqName(seqRanges1, seqName1, seqLen1)
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        if not range1: continue
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        range2 = rangeFromSeqName(seqRanges2, seqName2, seqLen2)
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        if not range2: continue
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        b = list(croppedBlocks(list(blocks), range1, range2))
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        if not b: continue
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        aln = seqName1, seqName2, b
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        alignments.append(aln)
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        updateSeqs(opts.trim1, seqNames1, seqLimits1, seqName1, range1, b, 0)
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        updateSeqs(opts.trim2, seqNames2, seqLimits2, seqName2, range2, b, 1)
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    return alignments, seqNames1, seqNames2, seqLimits1, seqLimits2
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def natural_sort_key(my_string):
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    '''Return a sort key for "natural" ordering, e.g. chr9 < chr10.'''
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    parts = re.split(r'(\d+)', my_string)
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    parts[1::2] = map(int, parts[1::2])
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    return parts
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def get_text_sizes(my_strings, font, fontsize, image_mode):
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    '''Get widths & heights, in pixels, of some strings.'''
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    if fontsize == 0: return [(0, 0) for i in my_strings]
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    image_size = 1, 1
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    im = Image.new(image_mode, image_size)
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    draw = ImageDraw.Draw(im)
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    return [draw.textsize(i, font=font) for i in my_strings]
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def sizeText(size):
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    suffixes = "bp", "kb", "Mb", "Gb"
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    for i, x in enumerate(suffixes):
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        j = 10 ** (i * 3)
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        if size < j * 10:
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            return "%.2g" % (1.0 * size / j) + x
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        if size < j * 1000 or i == len(suffixes) - 1:
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            return "%.0f" % (1.0 * size / j) + x
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def seqNameAndSizeText(seqName, seqSize):
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    return seqName + ": " + sizeText(seqSize)
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def getSeqInfo(sortOpt, seqNames, seqLimits,
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               font, fontsize, image_mode, isShowSize):
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    '''Return miscellaneous information about the sequences.'''
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    if sortOpt == 1:
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        seqNames.sort(key=natural_sort_key)
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    seqSizes = [seqLimits[i][1] - seqLimits[i][0] for i in seqNames]
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    if sortOpt == 2:
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        seqRecords = sorted(zip(seqSizes, seqNames), reverse=True)
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        seqSizes = [i[0] for i in seqRecords]
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        seqNames = [i[1] for i in seqRecords]
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    if isShowSize:
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        seqLabels = map(seqNameAndSizeText, seqNames, seqSizes)
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    else:
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        seqLabels = seqNames
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    labelSizes = get_text_sizes(seqLabels, font, fontsize, image_mode)
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    margin = max(zip(*labelSizes)[1])  # maximum text height
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    return seqNames, seqSizes, seqLabels, labelSizes, margin
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def div_ceil(x, y):
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    '''Return x / y rounded up.'''
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    q, r = divmod(x, y)
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    return q + (r != 0)
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def tot_seq_pix(seq_sizes, bp_per_pix):
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    '''Return the total pixels needed for sequences of the given sizes.'''
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    return sum([div_ceil(i, bp_per_pix) for i in seq_sizes])
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def get_bp_per_pix(seq_sizes, pix_tween_seqs, pix_limit):
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    '''Get the minimum bp-per-pixel that fits in the size limit.'''
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    seq_num = len(seq_sizes)
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    seq_pix_limit = pix_limit - pix_tween_seqs * (seq_num - 1)
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    if seq_pix_limit < seq_num:
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        raise Exception("can't fit the image: too many sequences?")
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    lower_bound = div_ceil(sum(seq_sizes), seq_pix_limit)
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    for bp_per_pix in itertools.count(lower_bound):  # slow linear search
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        if tot_seq_pix(seq_sizes, bp_per_pix) <= seq_pix_limit: break
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    return bp_per_pix
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def get_seq_starts(seq_pix, pix_tween_seqs, margin):
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    '''Get the start pixel for each sequence.'''
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    seq_starts = []
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    pix_tot = margin - pix_tween_seqs
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    for i in seq_pix:
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        pix_tot += pix_tween_seqs
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        seq_starts.append(pix_tot)
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        pix_tot += i
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    return seq_starts
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def get_pix_info(seq_sizes, bp_per_pix, pix_tween_seqs, margin):
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    '''Return pixel information about the sequences.'''
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    seq_pix = [div_ceil(i, bp_per_pix) for i in seq_sizes]
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    seq_starts = get_seq_starts(seq_pix, pix_tween_seqs, margin)
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    tot_pix = seq_starts[-1] + seq_pix[-1]
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    return seq_pix, seq_starts, tot_pix
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def drawLineForward(hits, width, bp_per_pix, beg1, beg2, size):
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    while True:
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        q1, r1 = divmod(beg1, bp_per_pix)
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        q2, r2 = divmod(beg2, bp_per_pix)
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        hits[q2 * width + q1] |= 1
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        next_pix = min(bp_per_pix - r1, bp_per_pix - r2)
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        if next_pix >= size: break
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        beg1 += next_pix
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        beg2 += next_pix
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        size -= next_pix
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def drawLineReverse(hits, width, bp_per_pix, beg1, beg2, size):
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    beg2 = -1 - beg2
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    while True:
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        q1, r1 = divmod(beg1, bp_per_pix)
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        q2, r2 = divmod(beg2, bp_per_pix)
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        hits[q2 * width + q1] |= 2
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        next_pix = min(bp_per_pix - r1, r2 + 1)
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        if next_pix >= size: break
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        beg1 += next_pix
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        beg2 -= next_pix
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        size -= next_pix
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def alignmentPixels(width, height, alignments, bp_per_pix, origins1, origins2):
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    hits = [0] * (width * height)  # the image data
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    for seq1, seq2, blocks in alignments:
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        ori1 = origins1[seq1]
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        ori2 = origins2[seq2]
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        for beg1, beg2, size in blocks:
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            if beg1 < 0:
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                beg1 = -(beg1 + size)
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                beg2 = -(beg2 + size)
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            if beg2 >= 0:
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                drawLineForward(hits, width, bp_per_pix,
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                                beg1 + ori1, beg2 + ori2, size)
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            else:
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                drawLineReverse(hits, width, bp_per_pix,
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                                beg1 + ori1, beg2 - ori2, size)
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    return hits
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def expandedSeqDict(seqDict):
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    '''Allow lookup by short sequence names, e.g. chr7 as well as hg19.chr7.'''
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    newDict = {}
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    for name, x in seqDict.items():
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        base = name.split(".")[-1]
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        newDict[name] = x
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        newDict[base] = x
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    return newDict
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def readBed(fileName, seqLimits):
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    if not fileName: return
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    for line in myOpen(fileName):
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        w = line.split()
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        if not w: continue
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        seqName = w[0]
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        if seqName not in seqLimits: continue
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        beg = int(w[1])
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        end = int(w[2])
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        layer = 900
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        color = "#ffe4ff"
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        if len(w) > 4:
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            if w[4] != ".":
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                layer = float(w[4])
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            if len(w) > 5:
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                if len(w) > 8 and w[8].count(",") == 2:
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                    color = "rgb(" + w[8] + ")"
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                elif w[5] == "+":
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                    color = "#fff4f4"
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                elif w[5] == "-":
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                    color = "#f4f4ff"
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        yield layer, color, seqName, beg, end
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def commaSeparatedInts(text):
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    return map(int, text.rstrip(",").split(","))
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def readGenePred(opts, fileName, seqLimits):
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    if not fileName: return
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    for line in myOpen(fileName):
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        fields = line.split()
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        if not fields: continue
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        if fields[2] not in "+-": fields = fields[1:]
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        seqName = fields[1]
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        if seqName not in seqLimits: continue
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        #strand = fields[2]
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        cdsBeg = int(fields[5])
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        cdsEnd = int(fields[6])
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        exonBegs = commaSeparatedInts(fields[8])
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        exonEnds = commaSeparatedInts(fields[9])
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        for beg, end in zip(exonBegs, exonEnds):
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            yield 300, opts.exon_color, seqName, beg, end
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            b = max(beg, cdsBeg)
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            e = min(end, cdsEnd)
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            if b < e: yield 400, opts.cds_color, seqName, b, e
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def readRmsk(fileName, seqLimits):
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    if not fileName: return
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    for line in myOpen(fileName):
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        fields = line.split()
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        if len(fields) == 17:  # rmsk.txt
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            seqName = fields[5]
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            if seqName not in seqLimits: continue  # do this ASAP for speed
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            beg = int(fields[6])
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            end = int(fields[7])
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            strand = fields[9]
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            repeatClass = fields[11]
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        elif len(fields) == 15:  # .out
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            seqName = fields[4]
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            if seqName not in seqLimits: continue
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            beg = int(fields[5]) - 1
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            end = int(fields[6])
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            strand = fields[8]
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            repeatClass = fields[10]
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        else:
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            continue
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        if repeatClass in ("Low_complexity", "Simple_repeat"):
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            yield 200, "#ffe4ff", seqName, beg, end
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        elif strand == "+":
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            yield 100, "#fff4f4", seqName, beg, end
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        else:
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            yield 100, "#f4f4ff", seqName, beg, end
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def isExtraFirstGapField(fields):
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    return fields[4].isdigit()
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def readGaps(opts, fileName, seqLimits):
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    '''Read locations of unsequenced gaps, from an agp or gap file.'''
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   363
    if not fileName: return
Martin@844
   364
    for line in myOpen(fileName):
Martin@650
   365
        w = line.split()
Martin@650
   366
        if not w or w[0][0] == "#": continue
Martin@650
   367
        if isExtraFirstGapField(w): w = w[1:]
Martin@650
   368
        if w[4] not in "NU": continue
Martin@650
   369
        seqName = w[0]
Martin@839
   370
        if seqName not in seqLimits: continue
Martin@650
   371
        end = int(w[2])
Martin@650
   372
        beg = end - int(w[5])  # zero-based coordinate
Martin@857
   373
        if w[7] == "yes":
Martin@859
   374
            yield 3000, opts.bridged_color, seqName, beg, end
Martin@857
   375
        else:
Martin@859
   376
            yield 2000, opts.unbridged_color, seqName, beg, end
Martin@650
   377
Martin@859
   378
def bedBoxes(beds, seqLimits, origins, margin, edge, isTop, bpPerPix):
Martin@857
   379
    for layer, color, seqName, beg, end in beds:
Martin@859
   380
        cropBeg, cropEnd = seqLimits[seqName]
Martin@859
   381
        beg = max(beg, cropBeg)
Martin@859
   382
        end = min(end, cropEnd)
Martin@859
   383
        if beg >= end: continue
Martin@845
   384
        ori = origins[seqName]
Martin@857
   385
        if layer <= 1000:
Martin@857
   386
            # include partly-covered pixels
Martin@857
   387
            b = (ori + beg) // bpPerPix
Martin@857
   388
            e = div_ceil(ori + end, bpPerPix)
Martin@857
   389
        else:
Martin@857
   390
            # exclude partly-covered pixels
Martin@857
   391
            b = div_ceil(ori + beg, bpPerPix)
Martin@857
   392
            e = (ori + end) // bpPerPix
Martin@857
   393
            if e <= b: continue
Martin@857
   394
        if isTop:
Martin@857
   395
            box = b, margin, e, edge
Martin@857
   396
        else:
Martin@857
   397
            box = margin, b, edge, e
Martin@857
   398
        yield layer, color, box
Martin@845
   399
Martin@857
   400
def drawAnnotations(im, boxes):
Martin@857
   401
    # xxx use partial transparency for different-color overlaps?
Martin@857
   402
    for layer, color, box in boxes:
Martin@650
   403
        im.paste(color, box)
Martin@650
   404
Martin@1
   405
def make_label(text, text_size, range_start, range_size):
Martin@1
   406
    '''Return an axis label with endpoint & sort-order information.'''
Martin@1
   407
    text_width  = text_size[0]
Martin@1
   408
    label_start = range_start + (range_size - text_width) // 2
Martin@1
   409
    label_end   = label_start + text_width
Martin@1
   410
    sort_key    = text_width - range_size
Martin@1
   411
    return sort_key, label_start, label_end, text
Martin@1
   412
Martin@645
   413
def get_nonoverlapping_labels(labels, label_space):
Martin@1
   414
    '''Get a subset of non-overlapping axis labels, greedily.'''
Martin@1
   415
    nonoverlapping_labels = []
Martin@1
   416
    for i in labels:
Martin@28
   417
        if True not in [i[1] < j[2] + label_space and j[1] < i[2] + label_space
Martin@28
   418
                        for j in nonoverlapping_labels]:
Martin@1
   419
            nonoverlapping_labels.append(i)
Martin@1
   420
    return nonoverlapping_labels
Martin@1
   421
Martin@837
   422
def get_axis_image(seqNames, name_sizes, seq_starts, seq_pix,
Martin@647
   423
                   font, image_mode, opts):
Martin@1
   424
    '''Make an image of axis labels.'''
Martin@1
   425
    min_pos = seq_starts[0]
Martin@1
   426
    max_pos = seq_starts[-1] + seq_pix[-1]
Martin@28
   427
    height = max(zip(*name_sizes)[1])
Martin@847
   428
    labels = map(make_label, seqNames, name_sizes, seq_starts, seq_pix)
Martin@1
   429
    labels = [i for i in labels if i[1] >= min_pos and i[2] <= max_pos]
Martin@1
   430
    labels.sort()
Martin@646
   431
    labels = get_nonoverlapping_labels(labels, opts.label_space)
Martin@1
   432
    image_size = max_pos, height
Martin@852
   433
    im = Image.new(image_mode, image_size, opts.border_color)
Martin@1
   434
    draw = ImageDraw.Draw(im)
Martin@1
   435
    for i in labels:
Martin@1
   436
        position = i[1], 0
Martin@646
   437
        draw.text(position, i[3], font=font, fill=opts.text_color)
Martin@1
   438
    return im
Martin@1
   439
Martin@839
   440
def seqOrigins(seqNames, seq_starts, seqLimits, bp_per_pix):
Martin@837
   441
    for i, j in zip(seqNames, seq_starts):
Martin@839
   442
        yield i, bp_per_pix * j - seqLimits[i][0]
Martin@836
   443
Martin@648
   444
def lastDotplot(opts, args):
Martin@643
   445
    if opts.fontfile:  font = ImageFont.truetype(opts.fontfile, opts.fontsize)
Martin@643
   446
    else:              font = ImageFont.load_default()
Martin@641
   447
Martin@643
   448
    image_mode = 'RGB'
Martin@643
   449
    forward_color = ImageColor.getcolor(opts.forwardcolor, image_mode)
Martin@643
   450
    reverse_color = ImageColor.getcolor(opts.reversecolor, image_mode)
Martin@643
   451
    zipped_colors = zip(forward_color, reverse_color)
Martin@643
   452
    overlap_color = tuple([(i + j) // 2 for i, j in zipped_colors])
Martin@641
   453
Martin@644
   454
    warn("reading alignments...")
Martin@851
   455
    alignmentInfo = readAlignments(args[0], opts)
Martin@851
   456
    alignments, seqNames1, seqNames2, seqLimits1, seqLimits2 = alignmentInfo
Martin@644
   457
    warn("done")
Martin@649
   458
    if not alignments: raise Exception("there are no alignments")
Martin@641
   459
Martin@851
   460
    i1 = getSeqInfo(opts.sort1, seqNames1, seqLimits1,
Martin@851
   461
                    font, opts.fontsize, image_mode, opts.lengths1)
Martin@850
   462
    seqNames1, seqSizes1, seqLabels1, labelSizes1, margin1 = i1
Martin@846
   463
Martin@851
   464
    i2 = getSeqInfo(opts.sort2, seqNames2, seqLimits2,
Martin@851
   465
                    font, opts.fontsize, image_mode, opts.lengths2)
Martin@850
   466
    seqNames2, seqSizes2, seqLabels2, labelSizes2, margin2 = i2
Martin@641
   467
Martin@644
   468
    warn("choosing bp per pixel...")
Martin@645
   469
    pix_limit1 = opts.width  - margin1
Martin@645
   470
    pix_limit2 = opts.height - margin2
Martin@855
   471
    bpPerPix1 = get_bp_per_pix(seqSizes1, opts.border_pixels, pix_limit1)
Martin@855
   472
    bpPerPix2 = get_bp_per_pix(seqSizes2, opts.border_pixels, pix_limit2)
Martin@855
   473
    bpPerPix = max(bpPerPix1, bpPerPix2)
Martin@855
   474
    warn("bp per pixel = " + str(bpPerPix))
Martin@641
   475
Martin@855
   476
    seq_pix1, seq_starts1, width  = get_pix_info(seqSizes1, bpPerPix,
Martin@852
   477
                                                 opts.border_pixels, margin1)
Martin@855
   478
    seq_pix2, seq_starts2, height = get_pix_info(seqSizes2, bpPerPix,
Martin@852
   479
                                                 opts.border_pixels, margin2)
Martin@847
   480
    warn("width:  " + str(width))
Martin@847
   481
    warn("height: " + str(height))
Martin@839
   482
Martin@855
   483
    origins1 = dict(seqOrigins(seqNames1, seq_starts1, seqLimits1, bpPerPix))
Martin@855
   484
    origins2 = dict(seqOrigins(seqNames2, seq_starts2, seqLimits2, bpPerPix))
Martin@641
   485
Martin@644
   486
    warn("processing alignments...")
Martin@855
   487
    hits = alignmentPixels(width, height, alignments, bpPerPix,
Martin@836
   488
                           origins1, origins2)
Martin@644
   489
    warn("done")
Martin@641
   490
Martin@643
   491
    image_size = width, height
Martin@646
   492
    im = Image.new(image_mode, image_size, opts.background_color)
Martin@134
   493
Martin@845
   494
    seqLimits1 = expandedSeqDict(seqLimits1)
Martin@845
   495
    seqLimits2 = expandedSeqDict(seqLimits2)
Martin@836
   496
    origins1 = expandedSeqDict(origins1)
Martin@836
   497
    origins2 = expandedSeqDict(origins2)
Martin@845
   498
Martin@857
   499
    beds1 = itertools.chain(readBed(opts.bed1, seqLimits1),
Martin@860
   500
                            readRmsk(opts.rmsk1, seqLimits1),
Martin@860
   501
                            readGenePred(opts, opts.genePred1, seqLimits1),
Martin@857
   502
                            readGaps(opts, opts.gap1, seqLimits1))
Martin@859
   503
    b1 = bedBoxes(beds1, seqLimits1, origins1, margin2, height, True, bpPerPix)
Martin@845
   504
Martin@857
   505
    beds2 = itertools.chain(readBed(opts.bed2, seqLimits2),
Martin@860
   506
                            readRmsk(opts.rmsk2, seqLimits2),
Martin@860
   507
                            readGenePred(opts, opts.genePred2, seqLimits2),
Martin@857
   508
                            readGaps(opts, opts.gap2, seqLimits2))
Martin@859
   509
    b2 = bedBoxes(beds2, seqLimits2, origins2, margin1, width, False, bpPerPix)
Martin@857
   510
Martin@857
   511
    boxes = sorted(itertools.chain(b1, b2))
Martin@857
   512
    drawAnnotations(im, boxes)
Martin@650
   513
Martin@643
   514
    for i in range(height):
Martin@643
   515
        for j in range(width):
Martin@643
   516
            store_value = hits[i * width + j]
Martin@643
   517
            xy = j, i
Martin@643
   518
            if   store_value == 1: im.putpixel(xy, forward_color)
Martin@643
   519
            elif store_value == 2: im.putpixel(xy, reverse_color)
Martin@643
   520
            elif store_value == 3: im.putpixel(xy, overlap_color)
Martin@95
   521
Martin@643
   522
    if opts.fontsize != 0:
Martin@846
   523
        axis1 = get_axis_image(seqLabels1, labelSizes1, seq_starts1, seq_pix1,
Martin@647
   524
                               font, image_mode, opts)
Martin@846
   525
        axis2 = get_axis_image(seqLabels2, labelSizes2, seq_starts2, seq_pix2,
Martin@647
   526
                               font, image_mode, opts)
Martin@834
   527
        axis2 = axis2.transpose(Image.ROTATE_270)  # !!! bug hotspot
Martin@643
   528
        im.paste(axis1, (0, 0))
Martin@643
   529
        im.paste(axis2, (0, 0))
Martin@1
   530
Martin@643
   531
    for i in seq_starts1[1:]:
Martin@852
   532
        box = i - opts.border_pixels, margin2, i, height
Martin@852
   533
        im.paste(opts.border_color, box)
Martin@1
   534
Martin@643
   535
    for i in seq_starts2[1:]:
Martin@852
   536
        box = margin1, i - opts.border_pixels, width, i
Martin@852
   537
        im.paste(opts.border_color, box)
Martin@1
   538
Martin@643
   539
    im.save(args[1])
Martin@648
   540
Martin@648
   541
if __name__ == "__main__":
Martin@649
   542
    usage = """%prog --help
Martin@649
   543
   or: %prog [options] maf-or-tab-alignments dotplot.png
Martin@649
   544
   or: %prog [options] maf-or-tab-alignments dotplot.gif
Martin@649
   545
   or: ..."""
Martin@649
   546
    description = "Draw a dotplot of pair-wise sequence alignments in MAF or tabular format."
Martin@649
   547
    op = optparse.OptionParser(usage=usage, description=description)
Martin@651
   548
    op.add_option("-1", "--seq1", metavar="PATTERN", action="append",
Martin@840
   549
                  default=[],
Martin@651
   550
                  help="which sequences to show from the 1st genome")
Martin@651
   551
    op.add_option("-2", "--seq2", metavar="PATTERN", action="append",
Martin@840
   552
                  default=[],
Martin@651
   553
                  help="which sequences to show from the 2nd genome")
Martin@648
   554
    # Replace "width" & "height" with a single "length" option?
Martin@648
   555
    op.add_option("-x", "--width", type="int", default=1000,
Martin@648
   556
                  help="maximum width in pixels (default: %default)")
Martin@648
   557
    op.add_option("-y", "--height", type="int", default=1000,
Martin@648
   558
                  help="maximum height in pixels (default: %default)")
Martin@649
   559
    op.add_option("-c", "--forwardcolor", metavar="COLOR", default="red",
Martin@649
   560
                  help="color for forward alignments (default: %default)")
Martin@649
   561
    op.add_option("-r", "--reversecolor", metavar="COLOR", default="blue",
Martin@649
   562
                  help="color for reverse alignments (default: %default)")
Martin@851
   563
    op.add_option("--sort1", type="int", default=1, metavar="N",
Martin@851
   564
                  help="genome1 sequence order: 0=input order, 1=name order, "
Martin@851
   565
                  "2=length order (default=%default)")
Martin@851
   566
    op.add_option("--sort2", type="int", default=1, metavar="N",
Martin@851
   567
                  help="genome2 sequence order: 0=input order, 1=name order, "
Martin@851
   568
                  "2=length order (default=%default)")
Martin@839
   569
    op.add_option("--trim1", action="store_true",
Martin@839
   570
                  help="trim unaligned sequence flanks from the 1st genome")
Martin@839
   571
    op.add_option("--trim2", action="store_true",
Martin@839
   572
                  help="trim unaligned sequence flanks from the 2nd genome")
Martin@852
   573
    op.add_option("--border-pixels", metavar="INT", type="int", default=1,
Martin@852
   574
                  help="number of pixels between sequences (default=%default)")
Martin@852
   575
    op.add_option("--border-color", metavar="COLOR", default="#dcdcdc",
Martin@852
   576
                  help="color for pixels between sequences (default=%default)")
Martin@852
   577
    # xxx --margin-color?
Martin@846
   578
Martin@850
   579
    og = optparse.OptionGroup(op, "Text options")
Martin@850
   580
    og.add_option("-f", "--fontfile", metavar="FILE",
Martin@850
   581
                  help="TrueType or OpenType font file")
Martin@850
   582
    og.add_option("-s", "--fontsize", metavar="SIZE", type="int", default=11,
Martin@850
   583
                  help="TrueType or OpenType font size (default: %default)")
Martin@850
   584
    og.add_option("--lengths1", action="store_true",
Martin@850
   585
                  help="show sequence lengths for the 1st (horizontal) genome")
Martin@850
   586
    og.add_option("--lengths2", action="store_true",
Martin@850
   587
                  help="show sequence lengths for the 2nd (vertical) genome")
Martin@850
   588
    op.add_option_group(og)
Martin@850
   589
Martin@860
   590
    og = optparse.OptionGroup(op, "Annotation options")
Martin@860
   591
    og.add_option("--bed1", metavar="FILE",
Martin@860
   592
                  help="read genome1 annotations from BED file")
Martin@860
   593
    og.add_option("--bed2", metavar="FILE",
Martin@860
   594
                  help="read genome2 annotations from BED file")
Martin@860
   595
    og.add_option("--rmsk1", metavar="FILE", help="read genome1 repeats from "
Martin@860
   596
                  "RepeatMasker .out or rmsk.txt file")
Martin@860
   597
    og.add_option("--rmsk2", metavar="FILE", help="read genome2 repeats from "
Martin@860
   598
                  "RepeatMasker .out or rmsk.txt file")
Martin@860
   599
    op.add_option_group(og)
Martin@860
   600
Martin@860
   601
    og = optparse.OptionGroup(op, "Gene options")
Martin@860
   602
    og.add_option("--genePred1", metavar="FILE",
Martin@860
   603
                  help="read genome1 genes from genePred file")
Martin@860
   604
    og.add_option("--genePred2", metavar="FILE",
Martin@860
   605
                  help="read genome2 genes from genePred file")
Martin@860
   606
    og.add_option("--exon-color", metavar="COLOR", default="#dfd",
Martin@860
   607
                  help="color for exons (default=%default)")
Martin@860
   608
    og.add_option("--cds-color", metavar="COLOR", default="#bdb",
Martin@860
   609
                  help="color for protein-coding regions (default=%default)")
Martin@860
   610
    op.add_option_group(og)
Martin@860
   611
Martin@650
   612
    og = optparse.OptionGroup(op, "Unsequenced gap options")
Martin@650
   613
    og.add_option("--gap1", metavar="FILE",
Martin@650
   614
                  help="read genome1 unsequenced gaps from agp or gap file")
Martin@650
   615
    og.add_option("--gap2", metavar="FILE",
Martin@650
   616
                  help="read genome2 unsequenced gaps from agp or gap file")
Martin@650
   617
    og.add_option("--bridged-color", metavar="COLOR", default="yellow",
Martin@650
   618
                  help="color for bridged gaps (default: %default)")
Martin@650
   619
    og.add_option("--unbridged-color", metavar="COLOR", default="pink",
Martin@650
   620
                  help="color for unbridged gaps (default: %default)")
Martin@650
   621
    op.add_option_group(og)
Martin@648
   622
    (opts, args) = op.parse_args()
Martin@648
   623
    if len(args) != 2: op.error("2 arguments needed")
Martin@648
   624
Martin@648
   625
    opts.text_color = "black"
Martin@648
   626
    opts.background_color = "white"
Martin@648
   627
    opts.label_space = 5     # minimum number of pixels between axis labels
Martin@648
   628
Martin@649
   629
    try: lastDotplot(opts, args)
Martin@649
   630
    except KeyboardInterrupt: pass  # avoid silly error message
Martin@649
   631
    except Exception, e:
Martin@649
   632
        prog = os.path.basename(sys.argv[0])
Martin@649
   633
        sys.exit(prog + ": error: " + str(e))