diff bin/last-dotplot @ 0:06f8460885ff

migrate from GitHub

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/last-dotplot	Sun Apr 19 20:51:13 2015 +0900
@@ -0,0 +1,291 @@
+#! /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
+
+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."""
+parser = optparse.OptionParser(usage=usage)
+# Replace "width" & "height" with a single "length" option?
+parser.add_option("-x", "--width", type="int", dest="width", default=1000,
+                  help="maximum width in pixels (default: %default)")
+parser.add_option("-y", "--height", type="int", dest="height", default=1000,
+                  help="maximum height in pixels (default: %default)")
+parser.add_option("-f", "--fontfile", dest="fontfile",
+                  help="TrueType or OpenType font file")
+parser.add_option("-s", "--fontsize", type="int", dest="fontsize", default=11,
+                  help="TrueType or OpenType font size (default: %default)")
+parser.add_option("-c", "--forwardcolor", dest="forwardcolor", default="red",
+                  help="Color for forward alignments (default: %default)")
+parser.add_option("-r", "--reversecolor", dest="reversecolor", default="blue",
+                  help="Color for reverse alignments (default: %default)")
+(opts, args) = parser.parse_args()
+if len(args) != 2: parser.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 to use 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)
+overlap_color = tuple([(i+j)//2 for i, j in zip(forward_color, reverse_color)])
+
+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
+
+sys.stderr.write(my_name + ": reading alignments...\n")
+input = fileinput.input(args[0])
+alignments, seq_size_dic1, seq_size_dic2 = readAlignments(input)
+sys.stderr.write(my_name + ": done\n")
+
+if not alignments:
+    sys.exit(my_name + ": there are no alignments")
+
+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
+
+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)
+
+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
+
+sys.stderr.write(my_name + ": choosing bp per pixel...\n")
+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)
+sys.stderr.write(my_name + ": bp per pixel = " + str(bp_per_pix) + "\n")
+
+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
+
+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))
+hits = [0] * (width * height)  # the image data
+
+sys.stderr.write(my_name + ": processing alignments...\n")
+for seq1, seq2, blocks in alignments:
+    seq_start1 = seq_start_dic1[seq1]
+    seq_start2 = seq_start_dic2[seq2]
+    my_start = seq_start2 * width + seq_start1
+    for beg1, beg2, size in blocks:
+        end1 = beg1 + size
+        end2 = beg2 + size
+        if beg1 >= 0: j = xrange(beg1, end1)
+        else:         j = xrange(-1 - beg1, -1 - end1, -1)
+        if beg2 >= 0: k = xrange(beg2, end2)
+        else:         k = xrange(-1 - beg2, -1 - end2, -1)
+        if beg2 >= 0: store_value = 1
+        else:         store_value = 2
+        for real_pos1, real_pos2 in itertools.izip(j, k):
+            pix1 = real_pos1 // bp_per_pix
+            pix2 = real_pos2 // bp_per_pix
+            hits[my_start + pix2 * width + pix1] |= store_value
+sys.stderr.write(my_name + ": done\n")
+
+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
+
+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])