scripts/last-dotplot
author Martin C. Frith
Wed Nov 08 12:17:50 2017 +0900 (2017-11-08)
changeset 905 8d52cef22afa
parent 904 c2f50cd4e29d
child 906 21fbf377641f
permissions -rwxr-xr-x
Refactor last-dotplot
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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 gzip
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from fnmatch import fnmatchcase
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import subprocess
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import 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 is None:
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        return []
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    if fileName == "-":
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        return sys.stdin
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    if fileName.endswith(".gz"):
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        return gzip.open(fileName)
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    return open(fileName)
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def warn(message):
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    if opts.verbose:
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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 seqRequestFromText(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(seqRequests, name, seqLen):
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    if not seqRequests: 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 seqRequests:
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        if fnmatchcase(name, pat) or 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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    seqRequests1 = map(seqRequestFromText, opts.seq1)
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    seqRequests2 = map(seqRequestFromText, 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(seqRequests1, seqName1, seqLen1)
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        if not range1: continue
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        range2 = rangeFromSeqName(seqRequests2, 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 prettyNum(n):
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    t = str(n)
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    groups = []
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    while t:
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        groups.append(t[-3:])
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        t = t[:-3]
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    return ",".join(reversed(groups))
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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 labelText(seqRange, labelOpt):
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    seqName, beg, end = seqRange
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    if labelOpt == 1:
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        return seqName + ": " + sizeText(end - beg)
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    if labelOpt == 2:
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        return seqName + ":" + prettyNum(beg) + ": " + sizeText(end - beg)
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    if labelOpt == 3:
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        return seqName + ":" + prettyNum(beg) + "-" + prettyNum(end)
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    return seqName
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def rangeLabels(seqRanges, labelOpt, font, fontsize, image_mode, textRot):
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    if fontsize:
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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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    x = y = 0
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    for r in seqRanges:
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        text = labelText(r, labelOpt)
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        if fontsize:
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            x, y = draw.textsize(text, font=font)
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            if textRot:
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                x, y = y, x
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        yield text, x, y
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def getSeqInfo(sortOpt, seqNames, seqLimits,
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               font, fontsize, image_mode, labelOpt, textRot):
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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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    for i in seqNames:
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        r = seqLimits[i]
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        out = i, str(r[0]), str(r[1])
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        warn("\t".join(out))
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    warn("")
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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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    seqRanges = [(i, seqLimits[i][0], seqLimits[i][1]) for i in seqNames]
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    labelData = list(rangeLabels(seqRanges, labelOpt,
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                                 font, fontsize, image_mode, textRot))
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    margin = max(i[2] for i in labelData)
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    # xxx the margin may be too big, because some labels may get omitted
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    return seqNames, seqSizes, labelData, 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 get_bp_per_pix(rangeSizes, pixTweenRanges, maxPixels):
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    '''Get the minimum bp-per-pixel that fits in the size limit.'''
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    warn("choosing bp per pixel...")
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    numOfRanges = len(rangeSizes)
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    maxPixelsInRanges = maxPixels - pixTweenRanges * (numOfRanges - 1)
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    if maxPixelsInRanges < numOfRanges:
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        raise Exception("can't fit the image: too many sequences?")
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    negLimit = -maxPixelsInRanges
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    negBpPerPix = sum(rangeSizes) // negLimit
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    while True:
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        if sum(i // negBpPerPix for i in rangeSizes) >= negLimit:
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            return -negBpPerPix
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        negBpPerPix -= 1
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def getRangePixBegs(rangePixLens, pixTweenRanges, margin):
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    '''Get the start pixel for each range.'''
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    rangePixBegs = []
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    pix_tot = margin - pixTweenRanges
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    for i in rangePixLens:
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        pix_tot += pixTweenRanges
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        rangePixBegs.append(pix_tot)
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        pix_tot += i
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    return rangePixBegs
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def pixelData(rangeSizes, bp_per_pix, pixTweenRanges, margin):
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    '''Return pixel information about the ranges.'''
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    rangePixLens = [div_ceil(i, bp_per_pix) for i in rangeSizes]
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    rangePixBegs = getRangePixBegs(rangePixLens, pixTweenRanges, margin)
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    tot_pix = rangePixBegs[-1] + rangePixLens[-1]
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    return rangePixBegs, rangePixLens, 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 findOrigin(ranges, beg, size):
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    if beg < 0:
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        beg = -(beg + size)
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    for rangeBeg, rangeEnd, origin in ranges:
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        if rangeEnd > beg:
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            return origin
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def alignmentPixels(width, height, alignments, bp_per_pix,
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                    rangeDict1, rangeDict2):
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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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        beg1, beg2, size = blocks[0]
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        ori1 = findOrigin(rangeDict1[seq1], beg1, size)
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        ori2 = findOrigin(rangeDict2[seq2], beg2, size)
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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 = seqDict.copy()
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    for name, x in seqDict.items():
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        if "." in name:
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            base = name.split(".")[-1]
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            if base in newDict:  # an ambiguous case was found:
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                return seqDict   # so give up completely
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            newDict[base] = x
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    return newDict
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def readBed(fileName, rangeDict):
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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 rangeDict: 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 = "#fbf"
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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 = "#ffe8e8"
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                elif w[5] == "-":
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                    color = "#e8e8ff"
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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, rangeDict):
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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 rangeDict: 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
Martin@860
   368
            b = max(beg, cdsBeg)
Martin@860
   369
            e = min(end, cdsEnd)
Martin@860
   370
            if b < e: yield 400, opts.cds_color, seqName, b, e
Martin@860
   371
Martin@905
   372
def readRmsk(fileName, rangeDict):
Martin@860
   373
    for line in myOpen(fileName):
Martin@860
   374
        fields = line.split()
Martin@860
   375
        if len(fields) == 17:  # rmsk.txt
Martin@860
   376
            seqName = fields[5]
Martin@905
   377
            if seqName not in rangeDict: continue  # do this ASAP for speed
Martin@860
   378
            beg = int(fields[6])
Martin@860
   379
            end = int(fields[7])
Martin@860
   380
            strand = fields[9]
Martin@860
   381
            repeatClass = fields[11]
Martin@860
   382
        elif len(fields) == 15:  # .out
Martin@860
   383
            seqName = fields[4]
Martin@905
   384
            if seqName not in rangeDict: continue
Martin@860
   385
            beg = int(fields[5]) - 1
Martin@860
   386
            end = int(fields[6])
Martin@860
   387
            strand = fields[8]
Martin@860
   388
            repeatClass = fields[10]
Martin@860
   389
        else:
Martin@860
   390
            continue
Martin@860
   391
        if repeatClass in ("Low_complexity", "Simple_repeat"):
Martin@895
   392
            yield 200, "#fbf", seqName, beg, end
Martin@860
   393
        elif strand == "+":
Martin@895
   394
            yield 100, "#ffe8e8", seqName, beg, end
Martin@860
   395
        else:
Martin@895
   396
            yield 100, "#e8e8ff", seqName, beg, end
Martin@860
   397
Martin@650
   398
def isExtraFirstGapField(fields):
Martin@650
   399
    return fields[4].isdigit()
Martin@650
   400
Martin@905
   401
def readGaps(opts, fileName, rangeDict):
Martin@650
   402
    '''Read locations of unsequenced gaps, from an agp or gap file.'''
Martin@844
   403
    for line in myOpen(fileName):
Martin@650
   404
        w = line.split()
Martin@650
   405
        if not w or w[0][0] == "#": continue
Martin@650
   406
        if isExtraFirstGapField(w): w = w[1:]
Martin@650
   407
        if w[4] not in "NU": continue
Martin@650
   408
        seqName = w[0]
Martin@905
   409
        if seqName not in rangeDict: continue
Martin@650
   410
        end = int(w[2])
Martin@650
   411
        beg = end - int(w[5])  # zero-based coordinate
Martin@857
   412
        if w[7] == "yes":
Martin@859
   413
            yield 3000, opts.bridged_color, seqName, beg, end
Martin@857
   414
        else:
Martin@859
   415
            yield 2000, opts.unbridged_color, seqName, beg, end
Martin@650
   416
Martin@905
   417
def bedBoxes(beds, rangeDict, margin, edge, isTop, bpPerPix):
Martin@897
   418
    for layer, color, seqName, bedBeg, bedEnd in beds:
Martin@905
   419
        for rangeBeg, rangeEnd, origin in rangeDict[seqName]:
Martin@905
   420
            beg = max(bedBeg, rangeBeg)
Martin@905
   421
            end = min(bedEnd, rangeEnd)
Martin@905
   422
            if beg >= end: continue
Martin@905
   423
            if layer <= 1000:
Martin@905
   424
                # include partly-covered pixels
Martin@905
   425
                b = (origin + beg) // bpPerPix
Martin@905
   426
                e = div_ceil(origin + end, bpPerPix)
Martin@905
   427
            else:
Martin@905
   428
                # exclude partly-covered pixels
Martin@905
   429
                b = div_ceil(origin + beg, bpPerPix)
Martin@905
   430
                e = (origin + end) // bpPerPix
Martin@905
   431
                if e <= b: continue
Martin@905
   432
            if isTop:
Martin@905
   433
                box = b, margin, e, edge
Martin@905
   434
            else:
Martin@905
   435
                box = margin, b, edge, e
Martin@905
   436
            yield layer, color, box
Martin@845
   437
Martin@857
   438
def drawAnnotations(im, boxes):
Martin@857
   439
    # xxx use partial transparency for different-color overlaps?
Martin@857
   440
    for layer, color, box in boxes:
Martin@650
   441
        im.paste(color, box)
Martin@650
   442
Martin@901
   443
def placedLabels(labels, rangePixBegs, rangePixLens, beg, end):
Martin@901
   444
    '''Return axis labels with endpoint & sort-order information.'''
Martin@901
   445
    maxWidth = end - beg
Martin@901
   446
    for i, j, k in zip(labels, rangePixBegs, rangePixLens):
Martin@901
   447
        text, textWidth, textHeight = i
Martin@901
   448
        if textWidth > maxWidth:
Martin@901
   449
            continue
Martin@901
   450
        labelBeg = j + (k - textWidth) // 2
Martin@901
   451
        labelEnd = labelBeg + textWidth
Martin@901
   452
        sortKey = textWidth - k
Martin@901
   453
        if labelBeg < beg:
Martin@904
   454
            sortKey += maxWidth * (beg - labelBeg)
Martin@901
   455
            labelBeg = beg
Martin@901
   456
            labelEnd = beg + textWidth
Martin@901
   457
        if labelEnd > end:
Martin@904
   458
            sortKey += maxWidth * (labelEnd - end)
Martin@901
   459
            labelEnd = end
Martin@901
   460
            labelBeg = end - textWidth
Martin@901
   461
        yield sortKey, labelBeg, labelEnd, text, textHeight
Martin@1
   462
Martin@897
   463
def nonoverlappingLabels(labels, minPixTweenLabels):
Martin@1
   464
    '''Get a subset of non-overlapping axis labels, greedily.'''
Martin@897
   465
    out = []
Martin@1
   466
    for i in labels:
Martin@897
   467
        beg = i[1] - minPixTweenLabels
Martin@897
   468
        end = i[2] + minPixTweenLabels
Martin@897
   469
        if all(j[2] <= beg or j[1] >= end for j in out):
Martin@897
   470
            out.append(i)
Martin@897
   471
    return out
Martin@1
   472
Martin@901
   473
def axisImage(labels, rangePixBegs, rangePixLens, textRot,
Martin@895
   474
              textAln, font, image_mode, opts):
Martin@1
   475
    '''Make an image of axis labels.'''
Martin@900
   476
    beg = rangePixBegs[0]
Martin@900
   477
    end = rangePixBegs[-1] + rangePixLens[-1]
Martin@901
   478
    margin = max(i[2] for i in labels)
Martin@901
   479
    labels = sorted(placedLabels(labels, rangePixBegs, rangePixLens, beg, end))
Martin@878
   480
    minPixTweenLabels = 0 if textRot else opts.label_space
Martin@897
   481
    labels = nonoverlappingLabels(labels, minPixTweenLabels)
Martin@897
   482
    image_size = (margin, end) if textRot else (end, margin)
Martin@895
   483
    im = Image.new(image_mode, image_size, opts.margin_color)
Martin@1
   484
    draw = ImageDraw.Draw(im)
Martin@1
   485
    for i in labels:
Martin@878
   486
        base = margin - i[4] if textAln else 0
Martin@878
   487
        position = (base, i[1]) if textRot else (i[1], base)
Martin@646
   488
        draw.text(position, i[3], font=font, fill=opts.text_color)
Martin@1
   489
    return im
Martin@1
   490
Martin@905
   491
def rangesPerSeq(seqNames, seqLimits, rangePixBegs, bpPerPix):
Martin@900
   492
    for i, j in zip(seqNames, rangePixBegs):
Martin@905
   493
        beg, end = seqLimits[i]
Martin@905
   494
        origin = bpPerPix * j - beg
Martin@905
   495
        r = beg, end, origin
Martin@905
   496
        yield i, [r]
Martin@836
   497
Martin@903
   498
def getFont(opts):
Martin@903
   499
    if opts.fontfile:
Martin@903
   500
        return ImageFont.truetype(opts.fontfile, opts.fontsize)
Martin@903
   501
    fileNames = []
Martin@903
   502
    try:
Martin@903
   503
        x = ["fc-match", "-f%{file}", "arial"]
Martin@903
   504
        p = subprocess.Popen(x, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
Martin@903
   505
        out, err = p.communicate()
Martin@903
   506
        fileNames.append(out)
Martin@903
   507
    except OSError as e:
Martin@903
   508
        warn("fc-match error: " + str(e))
Martin@903
   509
    fileNames.append("/Library/Fonts/Arial.ttf")  # for Mac
Martin@903
   510
    for i in fileNames:
Martin@903
   511
        try:
Martin@903
   512
            font = ImageFont.truetype(i, opts.fontsize)
Martin@903
   513
            warn("font: " + i)
Martin@903
   514
            return font
Martin@903
   515
        except IOError as e:
Martin@903
   516
            warn("font load error: " + str(e))
Martin@903
   517
    return ImageFont.load_default()
Martin@903
   518
Martin@648
   519
def lastDotplot(opts, args):
Martin@903
   520
    font = getFont(opts)
Martin@643
   521
    image_mode = 'RGB'
Martin@643
   522
    forward_color = ImageColor.getcolor(opts.forwardcolor, image_mode)
Martin@643
   523
    reverse_color = ImageColor.getcolor(opts.reversecolor, image_mode)
Martin@643
   524
    zipped_colors = zip(forward_color, reverse_color)
Martin@643
   525
    overlap_color = tuple([(i + j) // 2 for i, j in zipped_colors])
Martin@641
   526
Martin@644
   527
    warn("reading alignments...")
Martin@904
   528
    alnData = readAlignments(args[0], opts)
Martin@904
   529
    alignments, seqNames1, seqNames2, seqLimits1, seqLimits2 = alnData
Martin@644
   530
    warn("done")
Martin@649
   531
    if not alignments: raise Exception("there are no alignments")
Martin@641
   532
Martin@878
   533
    textRot1 = "vertical".startswith(opts.rot1)
Martin@851
   534
    i1 = getSeqInfo(opts.sort1, seqNames1, seqLimits1,
Martin@898
   535
                    font, opts.fontsize, image_mode, opts.labels1, textRot1)
Martin@899
   536
    seqNames1, rangeSizes1, labelData1, tMargin = i1
Martin@846
   537
Martin@878
   538
    textRot2 = "horizontal".startswith(opts.rot2)
Martin@851
   539
    i2 = getSeqInfo(opts.sort2, seqNames2, seqLimits2,
Martin@898
   540
                    font, opts.fontsize, image_mode, opts.labels2, textRot2)
Martin@899
   541
    seqNames2, rangeSizes2, labelData2, lMargin = i2
Martin@641
   542
Martin@896
   543
    maxPixels1 = opts.width  - lMargin
Martin@896
   544
    maxPixels2 = opts.height - tMargin
Martin@897
   545
    bpPerPix1 = get_bp_per_pix(rangeSizes1, opts.border_pixels, maxPixels1)
Martin@897
   546
    bpPerPix2 = get_bp_per_pix(rangeSizes2, opts.border_pixels, maxPixels2)
Martin@855
   547
    bpPerPix = max(bpPerPix1, bpPerPix2)
Martin@855
   548
    warn("bp per pixel = " + str(bpPerPix))
Martin@641
   549
Martin@900
   550
    p1 = pixelData(rangeSizes1, bpPerPix, opts.border_pixels, lMargin)
Martin@900
   551
    rangePixBegs1, rangePixLens1, width = p1
Martin@905
   552
    rangeDict1 = dict(rangesPerSeq(seqNames1, seqLimits1, rangePixBegs1,
Martin@905
   553
                                   bpPerPix))
Martin@900
   554
Martin@900
   555
    p2 = pixelData(rangeSizes2, bpPerPix, opts.border_pixels, tMargin)
Martin@900
   556
    rangePixBegs2, rangePixLens2, height = p2
Martin@905
   557
    rangeDict2 = dict(rangesPerSeq(seqNames2, seqLimits2, rangePixBegs2,
Martin@905
   558
                                   bpPerPix))
Martin@900
   559
Martin@847
   560
    warn("width:  " + str(width))
Martin@847
   561
    warn("height: " + str(height))
Martin@839
   562
Martin@644
   563
    warn("processing alignments...")
Martin@855
   564
    hits = alignmentPixels(width, height, alignments, bpPerPix,
Martin@905
   565
                           rangeDict1, rangeDict2)
Martin@641
   566
Martin@904
   567
    warn("reading annotations...")
Martin@134
   568
Martin@905
   569
    rangeDict1 = expandedSeqDict(rangeDict1)
Martin@905
   570
    beds1 = itertools.chain(readBed(opts.bed1, rangeDict1),
Martin@905
   571
                            readRmsk(opts.rmsk1, rangeDict1),
Martin@905
   572
                            readGenePred(opts, opts.genePred1, rangeDict1),
Martin@905
   573
                            readGaps(opts, opts.gap1, rangeDict1))
Martin@905
   574
    b1 = bedBoxes(beds1, rangeDict1, tMargin, height, True, bpPerPix)
Martin@845
   575
Martin@905
   576
    rangeDict2 = expandedSeqDict(rangeDict2)
Martin@905
   577
    beds2 = itertools.chain(readBed(opts.bed2, rangeDict2),
Martin@905
   578
                            readRmsk(opts.rmsk2, rangeDict2),
Martin@905
   579
                            readGenePred(opts, opts.genePred2, rangeDict2),
Martin@905
   580
                            readGaps(opts, opts.gap2, rangeDict2))
Martin@905
   581
    b2 = bedBoxes(beds2, rangeDict2, lMargin, width, False, bpPerPix)
Martin@857
   582
Martin@857
   583
    boxes = sorted(itertools.chain(b1, b2))
Martin@904
   584
Martin@904
   585
    warn("drawing...")
Martin@904
   586
Martin@904
   587
    image_size = width, height
Martin@904
   588
    im = Image.new(image_mode, image_size, opts.background_color)
Martin@904
   589
Martin@857
   590
    drawAnnotations(im, boxes)
Martin@650
   591
Martin@643
   592
    for i in range(height):
Martin@643
   593
        for j in range(width):
Martin@643
   594
            store_value = hits[i * width + j]
Martin@643
   595
            xy = j, i
Martin@643
   596
            if   store_value == 1: im.putpixel(xy, forward_color)
Martin@643
   597
            elif store_value == 2: im.putpixel(xy, reverse_color)
Martin@643
   598
            elif store_value == 3: im.putpixel(xy, overlap_color)
Martin@95
   599
Martin@643
   600
    if opts.fontsize != 0:
Martin@900
   601
        axis1 = axisImage(labelData1, rangePixBegs1, rangePixLens1,
Martin@895
   602
                          textRot1, False, font, image_mode, opts)
Martin@878
   603
        if textRot1:
Martin@878
   604
            axis1 = axis1.transpose(Image.ROTATE_90)
Martin@900
   605
        axis2 = axisImage(labelData2, rangePixBegs2, rangePixLens2,
Martin@895
   606
                          textRot2, textRot2, font, image_mode, opts)
Martin@878
   607
        if not textRot2:
Martin@878
   608
            axis2 = axis2.transpose(Image.ROTATE_270)
Martin@643
   609
        im.paste(axis1, (0, 0))
Martin@643
   610
        im.paste(axis2, (0, 0))
Martin@1
   611
Martin@900
   612
    for i in rangePixBegs1[1:]:
Martin@877
   613
        box = i - opts.border_pixels, tMargin, i, height
Martin@852
   614
        im.paste(opts.border_color, box)
Martin@1
   615
Martin@900
   616
    for i in rangePixBegs2[1:]:
Martin@877
   617
        box = lMargin, i - opts.border_pixels, width, i
Martin@852
   618
        im.paste(opts.border_color, box)
Martin@1
   619
Martin@643
   620
    im.save(args[1])
Martin@648
   621
Martin@648
   622
if __name__ == "__main__":
Martin@649
   623
    usage = """%prog --help
Martin@649
   624
   or: %prog [options] maf-or-tab-alignments dotplot.png
Martin@649
   625
   or: %prog [options] maf-or-tab-alignments dotplot.gif
Martin@649
   626
   or: ..."""
Martin@649
   627
    description = "Draw a dotplot of pair-wise sequence alignments in MAF or tabular format."
Martin@649
   628
    op = optparse.OptionParser(usage=usage, description=description)
Martin@866
   629
    op.add_option("-v", "--verbose", action="count",
Martin@866
   630
                  help="show progress messages & data about the plot")
Martin@651
   631
    op.add_option("-1", "--seq1", metavar="PATTERN", action="append",
Martin@840
   632
                  default=[],
Martin@651
   633
                  help="which sequences to show from the 1st genome")
Martin@651
   634
    op.add_option("-2", "--seq2", metavar="PATTERN", action="append",
Martin@840
   635
                  default=[],
Martin@651
   636
                  help="which sequences to show from the 2nd genome")
Martin@648
   637
    # Replace "width" & "height" with a single "length" option?
Martin@648
   638
    op.add_option("-x", "--width", type="int", default=1000,
Martin@648
   639
                  help="maximum width in pixels (default: %default)")
Martin@648
   640
    op.add_option("-y", "--height", type="int", default=1000,
Martin@648
   641
                  help="maximum height in pixels (default: %default)")
Martin@649
   642
    op.add_option("-c", "--forwardcolor", metavar="COLOR", default="red",
Martin@649
   643
                  help="color for forward alignments (default: %default)")
Martin@649
   644
    op.add_option("-r", "--reversecolor", metavar="COLOR", default="blue",
Martin@649
   645
                  help="color for reverse alignments (default: %default)")
Martin@851
   646
    op.add_option("--sort1", type="int", default=1, metavar="N",
Martin@851
   647
                  help="genome1 sequence order: 0=input order, 1=name order, "
Martin@851
   648
                  "2=length order (default=%default)")
Martin@851
   649
    op.add_option("--sort2", type="int", default=1, metavar="N",
Martin@851
   650
                  help="genome2 sequence order: 0=input order, 1=name order, "
Martin@851
   651
                  "2=length order (default=%default)")
Martin@839
   652
    op.add_option("--trim1", action="store_true",
Martin@839
   653
                  help="trim unaligned sequence flanks from the 1st genome")
Martin@839
   654
    op.add_option("--trim2", action="store_true",
Martin@839
   655
                  help="trim unaligned sequence flanks from the 2nd genome")
Martin@852
   656
    op.add_option("--border-pixels", metavar="INT", type="int", default=1,
Martin@852
   657
                  help="number of pixels between sequences (default=%default)")
Martin@895
   658
    op.add_option("--border-color", metavar="COLOR", default="black",
Martin@852
   659
                  help="color for pixels between sequences (default=%default)")
Martin@895
   660
    op.add_option("--margin-color", metavar="COLOR", default="#dcdcdc",
Martin@895
   661
                  help="margin color")
Martin@846
   662
Martin@850
   663
    og = optparse.OptionGroup(op, "Text options")
Martin@850
   664
    og.add_option("-f", "--fontfile", metavar="FILE",
Martin@850
   665
                  help="TrueType or OpenType font file")
Martin@903
   666
    og.add_option("-s", "--fontsize", metavar="SIZE", type="int", default=14,
Martin@850
   667
                  help="TrueType or OpenType font size (default: %default)")
Martin@898
   668
    og.add_option("--labels1", type="int", default=0, metavar="N", help=
Martin@898
   669
                  "genome1 labels: 0=name, 1=name:length, "
Martin@898
   670
                  "2=name:start:length, 3=name:start-end (default=%default)")
Martin@898
   671
    og.add_option("--labels2", type="int", default=0, metavar="N", help=
Martin@898
   672
                  "genome2 labels: 0=name, 1=name:length, "
Martin@898
   673
                  "2=name:start:length, 3=name:start-end (default=%default)")
Martin@878
   674
    og.add_option("--rot1", metavar="ROT", default="h",
Martin@878
   675
                  help="text rotation for the 1st genome (default=%default)")
Martin@878
   676
    og.add_option("--rot2", metavar="ROT", default="v",
Martin@878
   677
                  help="text rotation for the 2nd genome (default=%default)")
Martin@850
   678
    op.add_option_group(og)
Martin@850
   679
Martin@860
   680
    og = optparse.OptionGroup(op, "Annotation options")
Martin@860
   681
    og.add_option("--bed1", metavar="FILE",
Martin@860
   682
                  help="read genome1 annotations from BED file")
Martin@860
   683
    og.add_option("--bed2", metavar="FILE",
Martin@860
   684
                  help="read genome2 annotations from BED file")
Martin@860
   685
    og.add_option("--rmsk1", metavar="FILE", help="read genome1 repeats from "
Martin@860
   686
                  "RepeatMasker .out or rmsk.txt file")
Martin@860
   687
    og.add_option("--rmsk2", metavar="FILE", help="read genome2 repeats from "
Martin@860
   688
                  "RepeatMasker .out or rmsk.txt file")
Martin@860
   689
    op.add_option_group(og)
Martin@860
   690
Martin@860
   691
    og = optparse.OptionGroup(op, "Gene options")
Martin@860
   692
    og.add_option("--genePred1", metavar="FILE",
Martin@860
   693
                  help="read genome1 genes from genePred file")
Martin@860
   694
    og.add_option("--genePred2", metavar="FILE",
Martin@860
   695
                  help="read genome2 genes from genePred file")
Martin@895
   696
    og.add_option("--exon-color", metavar="COLOR", default="PaleGreen",
Martin@860
   697
                  help="color for exons (default=%default)")
Martin@895
   698
    og.add_option("--cds-color", metavar="COLOR", default="LimeGreen",
Martin@860
   699
                  help="color for protein-coding regions (default=%default)")
Martin@860
   700
    op.add_option_group(og)
Martin@860
   701
Martin@650
   702
    og = optparse.OptionGroup(op, "Unsequenced gap options")
Martin@650
   703
    og.add_option("--gap1", metavar="FILE",
Martin@650
   704
                  help="read genome1 unsequenced gaps from agp or gap file")
Martin@650
   705
    og.add_option("--gap2", metavar="FILE",
Martin@650
   706
                  help="read genome2 unsequenced gaps from agp or gap file")
Martin@650
   707
    og.add_option("--bridged-color", metavar="COLOR", default="yellow",
Martin@650
   708
                  help="color for bridged gaps (default: %default)")
Martin@895
   709
    og.add_option("--unbridged-color", metavar="COLOR", default="orange",
Martin@650
   710
                  help="color for unbridged gaps (default: %default)")
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   711
    op.add_option_group(og)
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   712
    (opts, args) = op.parse_args()
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   713
    if len(args) != 2: op.error("2 arguments needed")
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   714
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   715
    opts.text_color = "black"
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   716
    opts.background_color = "white"
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   717
    opts.label_space = 5     # minimum number of pixels between axis labels
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   718
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   719
    try: lastDotplot(opts, args)
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   720
    except KeyboardInterrupt: pass  # avoid silly error message
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   721
    except Exception as e:
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   722
        prog = os.path.basename(sys.argv[0])
Martin@649
   723
        sys.exit(prog + ": error: " + str(e))