#! /usr/bin/env python

# Read pair-wise alignments in MAF or LAST tabular format: write an

# "Oxford grid", a.k.a. dotplot.

# TODO: Currently, pixels with zero aligned nt-pairs are white, and

# pixels with one or more aligned nt-pairs are black.  This can look

# too crowded for large genome alignments.  I tried shading each pixel

# according to the number of aligned nt-pairs within it, but the

# result is too faint.  How can this be done better?

import fileinput, itertools, optparse, os, re, sys

# Try to make PIL/PILLOW work:

try: from PIL import Image, ImageDraw, ImageFont, ImageColor

except ImportError: import Image, ImageDraw, ImageFont, ImageColor

def warn(message):

    prog = os.path.basename(sys.argv[0])

    sys.stderr.write(prog + ": " + message + "\n")

def tabBlocks(beg1, beg2, blocks):

    '''Get the gapless blocks of an alignment, from LAST tabular format.'''

    for i in blocks.split(","):

        if ":" in i:

            x, y = i.split(":")

            beg1 += int(x)

            beg2 += int(y)

        else:

            size = int(i)

            yield beg1, beg2, size

            beg1 += size

            beg2 += size

def mafBlocks(beg1, beg2, seq1, seq2):

    '''Get the gapless blocks of an alignment, from MAF format.'''

    size = 0

    for x, y in itertools.izip(seq1, seq2):

        if x == "-":

            if size:

                yield beg1, beg2, size

                beg1 += size

                beg2 += size

                size = 0

            beg2 += 1

        elif y == "-":

            if size:

                yield beg1, beg2, size

                beg1 += size

                beg2 += size

                size = 0

            beg1 += 1

        else:

            size += 1

    if size: yield beg1, beg2, size

def alignmentInput(lines):

    '''Get alignments and sequence lengths, from MAF or tabular format.'''

    mafCount = 0

    for line in lines:

        w = line.split()

        if line[0].isdigit():  # tabular format

            chr1, beg1, seqlen1 = w[1], int(w[2]), int(w[5])

            if w[4] == "-": beg1 -= seqlen1

            chr2, beg2, seqlen2 = w[6], int(w[7]), int(w[10])

            if w[9] == "-": beg2 -= seqlen2

            blocks = tabBlocks(beg1, beg2, w[11])

            yield chr1, seqlen1, chr2, seqlen2, blocks

        elif line[0] == "s":  # MAF format

            if mafCount == 0:

                chr1, beg1, seqlen1, seq1 = w[1], int(w[2]), int(w[5]), w[6]

                if w[4] == "-": beg1 -= seqlen1

                mafCount = 1

            else:

                chr2, beg2, seqlen2, seq2 = w[1], int(w[2]), int(w[5]), w[6]

                if w[4] == "-": beg2 -= seqlen2

                blocks = mafBlocks(beg1, beg2, seq1, seq2)

                yield chr1, seqlen1, chr2, seqlen2, blocks

                mafCount = 0

def readAlignments(lines):

    '''Get alignments and sequence lengths, from MAF or tabular format.'''

    alignments = []

    seqLengths1 = {}

    seqLengths2 = {}

    for chr1, seqlen1, chr2, seqlen2, blocks in alignmentInput(lines):

        aln = chr1, chr2, blocks

        alignments.append(aln)

        seqLengths1[chr1] = seqlen1

        seqLengths2[chr2] = seqlen2

    return alignments, seqLengths1, seqLengths2

def natural_sort_key(my_string):

    '''Return a sort key for "natural" ordering, e.g. chr9 < chr10.'''

    parts = re.split(r'(\d+)', my_string)

    parts[1::2] = map(int, parts[1::2])

    return parts

def get_text_sizes(my_strings):

    '''Get widths & heights, in pixels, of some strings.'''

    if opts.fontsize == 0: return [(0, 0) for i in my_strings]

    image_size = 1, 1

    im = Image.new(image_mode, image_size)

    draw = ImageDraw.Draw(im)

    return [draw.textsize(i, font=font) for i in my_strings]

def get_seq_info(seq_size_dic):

    '''Return miscellaneous information about the sequences.'''

    seq_names = seq_size_dic.keys()

    seq_names.sort(key=natural_sort_key)

    seq_sizes = [seq_size_dic[i] for i in seq_names]

    name_sizes = get_text_sizes(seq_names)

    margin = max(zip(*name_sizes)[1])  # maximum text height

    return seq_names, seq_sizes, name_sizes, margin

def div_ceil(x, y):

    '''Return x / y rounded up.'''

    q, r = divmod(x, y)

    return q + (r != 0)

def tot_seq_pix(seq_sizes, bp_per_pix):

    '''Return the total pixels needed for sequences of the given sizes.'''

    return sum([div_ceil(i, bp_per_pix) for i in seq_sizes])

def get_bp_per_pix(seq_sizes, pix_limit):

    '''Get the minimum bp-per-pixel that fits in the size limit.'''

    seq_num = len(seq_sizes)

    seq_pix_limit = pix_limit - pix_tween_seqs * (seq_num - 1)

    if seq_pix_limit < seq_num:

        sys.exit(my_name + ": can't fit the image: too many sequences?")

    lower_bound = div_ceil(sum(seq_sizes), seq_pix_limit)

    for bp_per_pix in itertools.count(lower_bound):  # slow linear search

        if tot_seq_pix(seq_sizes, bp_per_pix) <= seq_pix_limit: break

    return bp_per_pix

def get_seq_starts(seq_pix, pix_tween_seqs, margin):

    '''Get the start pixel for each sequence.'''

    seq_starts = []

    pix_tot = margin - pix_tween_seqs

    for i in seq_pix:

        pix_tot += pix_tween_seqs

        seq_starts.append(pix_tot)

        pix_tot += i

    return seq_starts

def get_pix_info(seq_sizes, margin):

    '''Return pixel information about the sequences.'''

    seq_pix = [div_ceil(i, bp_per_pix) for i in seq_sizes]

    seq_starts = get_seq_starts(seq_pix, pix_tween_seqs, margin)

    tot_pix = seq_starts[-1] + seq_pix[-1]

    return seq_pix, seq_starts, tot_pix

def drawLineForward(hits, width, bp_per_pix, origin, beg1, beg2, size):

    while True:

        q1, r1 = divmod(beg1, bp_per_pix)

        q2, r2 = divmod(beg2, bp_per_pix)

        hits[origin + q2 * width + q1] |= 1

        next_pix = min(bp_per_pix - r1, bp_per_pix - r2)

        if next_pix >= size: break

        beg1 += next_pix

        beg2 += next_pix

        size -= next_pix

def drawLineReverse(hits, width, bp_per_pix, origin, beg1, beg2, size):

    beg2 = -1 - beg2

    while True:

        q1, r1 = divmod(beg1, bp_per_pix)

        q2, r2 = divmod(beg2, bp_per_pix)

        hits[origin + q2 * width + q1] |= 2

        next_pix = min(bp_per_pix - r1, r2 + 1)

        if next_pix >= size: break

        beg1 += next_pix

        beg2 -= next_pix

        size -= next_pix

def alignmentPixels(width, height, alignments, bp_per_pix,

                    seq_start_dic1, seq_start_dic2):

    hits = [0] * (width * height)  # the image data

    for seq1, seq2, blocks in alignments:

        seq_start1 = seq_start_dic1[seq1]

        seq_start2 = seq_start_dic2[seq2]

        origin = seq_start2 * width + seq_start1

        for beg1, beg2, size in blocks:

            if beg1 < 0:

                beg1 = -(beg1 + size)

                beg2 = -(beg2 + size)

            if beg2 >= 0:

                drawLineForward(hits, width, bp_per_pix, origin,

                                beg1, beg2, size)

            else:

                drawLineReverse(hits, width, bp_per_pix, origin,

                                beg1, beg2, size)

    return hits

def make_label(text, text_size, range_start, range_size):

    '''Return an axis label with endpoint & sort-order information.'''

    text_width  = text_size[0]

    label_start = range_start + (range_size - text_width) // 2

    label_end   = label_start + text_width

    sort_key    = text_width - range_size

    return sort_key, label_start, label_end, text

def get_nonoverlapping_labels(labels):

    '''Get a subset of non-overlapping axis labels, greedily.'''

    nonoverlapping_labels = []

    for i in labels:

        if True not in [i[1] < j[2] + label_space and j[1] < i[2] + label_space

                        for j in nonoverlapping_labels]:

            nonoverlapping_labels.append(i)

    return nonoverlapping_labels

def get_axis_image(seq_names, name_sizes, seq_starts, seq_pix):

    '''Make an image of axis labels.'''

    min_pos = seq_starts[0]

    max_pos = seq_starts[-1] + seq_pix[-1]

    height = max(zip(*name_sizes)[1])

    labels = [make_label(i, j, k, l) for i, j, k, l in

              zip(seq_names, name_sizes, seq_starts, seq_pix)]

    labels = [i for i in labels if i[1] >= min_pos and i[2] <= max_pos]

    labels.sort()

    labels = get_nonoverlapping_labels(labels)

    image_size = max_pos, height

    im = Image.new(image_mode, image_size, border_shade)

    draw = ImageDraw.Draw(im)

    for i in labels:

        position = i[1], 0

        draw.text(position, i[3], font=font, fill=text_color)

    return im

if __name__ == "__main__":

    my_name = os.path.basename(sys.argv[0])

    usage = """

  %prog --help

  %prog [options] last-tabular-output dotplot.png

  %prog [options] last-tabular-output dotplot.gif

  etc."""

    op = optparse.OptionParser(usage=usage)

    # Replace "width" & "height" with a single "length" option?

    op.add_option("-x", "--width", type="int", default=1000,

                  help="maximum width in pixels (default: %default)")

    op.add_option("-y", "--height", type="int", default=1000,

                  help="maximum height in pixels (default: %default)")

    op.add_option("-f", "--fontfile",

                  help="TrueType or OpenType font file")

    op.add_option("-s", "--fontsize", type="int", default=11,

                  help="TrueType or OpenType font size (default: %default)")

    op.add_option("-c", "--forwardcolor", default="red",

                  help="Color for forward alignments (default: %default)")

    op.add_option("-r", "--reversecolor", default="blue",

                  help="Color for reverse alignments (default: %default)")

    (opts, args) = op.parse_args()

    if len(args) != 2: op.error("2 arguments needed")

    if opts.fontfile:  font = ImageFont.truetype(opts.fontfile, opts.fontsize)

    else:              font = ImageFont.load_default()

    # Make these options too?

    text_color = "black"

    background_color = "white"

    pix_tween_seqs = 2  # number of border pixels between sequences

    border_shade = 239, 239, 239  # the shade of grey for border pixels

    label_space = 5     # minimum number of pixels between axis labels

    image_mode = 'RGB'

    forward_color = ImageColor.getcolor(opts.forwardcolor, image_mode)

    reverse_color = ImageColor.getcolor(opts.reversecolor, image_mode)

    zipped_colors = zip(forward_color, reverse_color)

    overlap_color = tuple([(i + j) // 2 for i, j in zipped_colors])

    warn("reading alignments...")

    input = fileinput.input(args[0])

    alignments, seq_size_dic1, seq_size_dic2 = readAlignments(input)

    warn("done")

    if not alignments:

        sys.exit(my_name + ": there are no alignments")

    seq_names1, seq_sizes1, name_sizes1, margin1 = get_seq_info(seq_size_dic1)

    seq_names2, seq_sizes2, name_sizes2, margin2 = get_seq_info(seq_size_dic2)

    warn("choosing bp per pixel...")

    bp_per_pix1 = get_bp_per_pix(seq_sizes1, opts.width  - margin1)

    bp_per_pix2 = get_bp_per_pix(seq_sizes2, opts.height - margin2)

    bp_per_pix = max(bp_per_pix1, bp_per_pix2)

    warn("bp per pixel = " + str(bp_per_pix))

    seq_pix1, seq_starts1, width  = get_pix_info(seq_sizes1, margin1)

    seq_pix2, seq_starts2, height = get_pix_info(seq_sizes2, margin2)

    seq_start_dic1 = dict(zip(seq_names1, seq_starts1))

    seq_start_dic2 = dict(zip(seq_names2, seq_starts2))

    warn("processing alignments...")

    hits = alignmentPixels(width, height, alignments, bp_per_pix,

                           seq_start_dic1, seq_start_dic2)

    warn("done")

    image_size = width, height

    im = Image.new(image_mode, image_size, background_color)

    for i in range(height):

        for j in range(width):

            store_value = hits[i * width + j]

            xy = j, i

            if   store_value == 1: im.putpixel(xy, forward_color)

            elif store_value == 2: im.putpixel(xy, reverse_color)

            elif store_value == 3: im.putpixel(xy, overlap_color)

    if opts.fontsize != 0:

        axis1 = get_axis_image(seq_names1, name_sizes1, seq_starts1, seq_pix1)

        axis2 = get_axis_image(seq_names2, name_sizes2, seq_starts2, seq_pix2)

        axis2 = axis2.rotate(270)

        im.paste(axis1, (0, 0))

        im.paste(axis2, (0, 0))

    for i in seq_starts1[1:]:

        box = i - pix_tween_seqs, margin2, i, height

        im.paste(border_shade, box)

    for i in seq_starts2[1:]:

        box = margin1, i - pix_tween_seqs, width, i

        im.paste(border_shade, box)

    im.save(args[1])