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last-dotplot
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last-dotplot
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#! /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 collections
import functools
import gzip
from fnmatch import fnmatchcase
from operator import itemgetter
import subprocess
import 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 myOpen(fileName): # faster than fileinput
if fileName is None:
return []
if fileName == "-":
return sys.stdin
if fileName.endswith(".gz"):
return gzip.open(fileName)
return open(fileName)
def warn(message):
if opts.verbose:
prog = os.path.basename(sys.argv[0])
sys.stderr.write(prog + ": " + message + "\n")
def groupByFirstItem(things):
for k, v in itertools.groupby(things, itemgetter(0)):
yield k, [i[1:] for i in v]
def croppedBlocks(blocks, ranges1, ranges2):
headBeg1, headBeg2, headSize = blocks[0]
for r1 in ranges1:
for r2 in ranges2:
cropBeg1, cropEnd1 = r1
if headBeg1 < 0:
cropBeg1, cropEnd1 = -cropEnd1, -cropBeg1
cropBeg2, cropEnd2 = r2
if headBeg2 < 0:
cropBeg2, cropEnd2 = -cropEnd2, -cropBeg2
for beg1, beg2, size in blocks:
b1 = max(cropBeg1, beg1)
e1 = min(cropEnd1, beg1 + size)
if b1 >= e1: continue
offset = beg2 - beg1
b2 = max(cropBeg2, b1 + offset)
e2 = min(cropEnd2, e1 + offset)
if b2 >= e2: continue
yield b2 - offset, b2, e2 - b2
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 seqRequestFromText(text):
if ":" in text:
pattern, interval = text.rsplit(":", 1)
if "-" in interval:
beg, end = interval.rsplit("-", 1)
return pattern, int(beg), int(end) # beg may be negative
return text, 0, sys.maxsize
def rangesFromSeqName(seqRequests, name, seqLen):
if seqRequests:
base = name.split(".")[-1] # allow for names like hg19.chr7
for pat, beg, end in seqRequests:
if fnmatchcase(name, pat) or fnmatchcase(base, pat):
yield max(beg, 0), min(end, seqLen)
else:
yield 0, seqLen
def updateSeqs(coverDict, seqRanges, seqName, ranges, coveredRange):
beg, end = coveredRange
if beg < 0:
coveredRange = -end, -beg
if seqName in coverDict:
coverDict[seqName].append(coveredRange)
else:
coverDict[seqName] = [coveredRange]
for beg, end in ranges:
r = seqName, beg, end
seqRanges.append(r)
def readAlignments(fileName, opts):
'''Get alignments and sequence limits, from MAF or tabular format.'''
seqRequests1 = map(seqRequestFromText, opts.seq1)
seqRequests2 = map(seqRequestFromText, opts.seq2)
alignments = []
seqRanges1 = []
seqRanges2 = []
coverDict1 = {}
coverDict2 = {}
lines = myOpen(fileName)
for seqName1, seqLen1, seqName2, seqLen2, blocks in alignmentInput(lines):
ranges1 = sorted(rangesFromSeqName(seqRequests1, seqName1, seqLen1))
if not ranges1: continue
ranges2 = sorted(rangesFromSeqName(seqRequests2, seqName2, seqLen2))
if not ranges2: continue
b = list(croppedBlocks(list(blocks), ranges1, ranges2))
if not b: continue
aln = seqName1, seqName2, b
alignments.append(aln)
coveredRange1 = b[0][0], b[-1][0] + b[-1][2]
updateSeqs(coverDict1, seqRanges1, seqName1, ranges1, coveredRange1)
coveredRange2 = b[0][1], b[-1][1] + b[-1][2]
updateSeqs(coverDict2, seqRanges2, seqName2, ranges2, coveredRange2)
return alignments, seqRanges1, coverDict1, seqRanges2, coverDict2
def nameAndRangesFromDict(cropDict, seqName):
if seqName in cropDict:
return seqName, cropDict[seqName]
n = seqName.split(".")[-1]
if n in cropDict:
return n, cropDict[n]
return seqName, []
def rangesForSecondaryAlignments(primaryRanges, seqLen):
if primaryRanges:
return primaryRanges
return [(0, seqLen)]
def readSecondaryAlignments(opts, cropRanges1, cropRanges2):
cropDict1 = dict(groupByFirstItem(cropRanges1))
cropDict2 = dict(groupByFirstItem(cropRanges2))
alignments = []
seqRanges1 = []
seqRanges2 = []
coverDict1 = {}
coverDict2 = {}
lines = myOpen(opts.alignments)
for seqName1, seqLen1, seqName2, seqLen2, blocks in alignmentInput(lines):
seqName1, ranges1 = nameAndRangesFromDict(cropDict1, seqName1)
seqName2, ranges2 = nameAndRangesFromDict(cropDict2, seqName2)
if not ranges1 and not ranges2:
continue
r1 = rangesForSecondaryAlignments(ranges1, seqLen1)
r2 = rangesForSecondaryAlignments(ranges2, seqLen2)
b = list(croppedBlocks(list(blocks), r1, r2))
if not b: continue
aln = seqName1, seqName2, b
alignments.append(aln)
if not ranges1:
coveredRange1 = b[0][0], b[-1][0] + b[-1][2]
updateSeqs(coverDict1, seqRanges1, seqName1, r1, coveredRange1)
if not ranges2:
coveredRange2 = b[0][1], b[-1][1] + b[-1][2]
updateSeqs(coverDict2, seqRanges2, seqName2, r2, coveredRange2)
return alignments, seqRanges1, coverDict1, seqRanges2, coverDict2
def twoValuesFromOption(text, separator):
if separator in text:
return text.split(separator)
return text, text
def mergedRanges(ranges):
oldBeg, maxEnd = ranges[0]
for beg, end in ranges:
if beg > maxEnd:
yield oldBeg, maxEnd
oldBeg = beg
maxEnd = end
elif end > maxEnd:
maxEnd = end
yield oldBeg, maxEnd
def mergedRangesPerSeq(coverDict):
for k, v in coverDict.iteritems():
v.sort()
yield k, list(mergedRanges(v))
def coveredLength(mergedCoverDict):
return sum(sum(e - b for b, e in v) for v in mergedCoverDict.itervalues())
def trimmed(seqRanges, coverDict, minAlignedBases, maxGapFrac, endPad, midPad):
maxEndGapFrac, maxMidGapFrac = twoValuesFromOption(maxGapFrac, ",")
maxEndGap = max(float(maxEndGapFrac) * minAlignedBases, endPad * 1.0)
maxMidGap = max(float(maxMidGapFrac) * minAlignedBases, midPad * 2.0)
for seqName, rangeBeg, rangeEnd in seqRanges:
seqBlocks = coverDict[seqName]
blocks = [i for i in seqBlocks if i[0] < rangeEnd and i[1] > rangeBeg]
if blocks[0][0] - rangeBeg > maxEndGap:
rangeBeg = blocks[0][0] - endPad
for j, y in enumerate(blocks):
if j:
x = blocks[j - 1]
if y[0] - x[1] > maxMidGap:
yield seqName, rangeBeg, x[1] + midPad
rangeBeg = y[0] - midPad
if rangeEnd - blocks[-1][1] > maxEndGap:
rangeEnd = blocks[-1][1] + endPad
yield seqName, rangeBeg, rangeEnd
def rangesWithStrandInfo(seqRanges, strandOpt, alignments, seqIndex):
if strandOpt == "1":
forwardMinusReverse = collections.defaultdict(int)
for i in alignments:
blocks = i[2]
beg1, beg2, size = blocks[0]
numOfAlignedLetterPairs = sum(i[2] for i in blocks)
if (beg1 < 0) != (beg2 < 0): # opposite-strand alignment
numOfAlignedLetterPairs *= -1
forwardMinusReverse[i[seqIndex]] += numOfAlignedLetterPairs
strandNum = 0
for seqName, beg, end in seqRanges:
if strandOpt == "1":
strandNum = 1 if forwardMinusReverse[seqName] >= 0 else 2
yield seqName, beg, end, strandNum
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 nameKey(oneSeqRanges):
return natural_sort_key(oneSeqRanges[0][0])
def sizeKey(oneSeqRanges):
return sum(b - e for n, b, e, s in oneSeqRanges), nameKey(oneSeqRanges)
def alignmentKey(seqNamesToLists, oneSeqRanges):
seqName = oneSeqRanges[0][0]
alignmentsOfThisSequence = seqNamesToLists[seqName]
numOfAlignedLetterPairs = sum(i[3] for i in alignmentsOfThisSequence)
toMiddle = numOfAlignedLetterPairs // 2
for i in alignmentsOfThisSequence:
toMiddle -= i[3]
if toMiddle < 0:
return i[1:3] # sequence-rank and "position" of this alignment
def rankAndFlipPerSeq(seqRanges):
rangesGroupedBySeqName = itertools.groupby(seqRanges, itemgetter(0))
for rank, group in enumerate(rangesGroupedBySeqName):
seqName, ranges = group
strandNum = next(ranges)[3]
flip = 1 if strandNum < 2 else -1
yield seqName, (rank, flip)
def alignmentSortData(alignments, seqIndex, otherNamesToRanksAndFlips):
otherIndex = 1 - seqIndex
for i in alignments:
blocks = i[2]
otherRank, otherFlip = otherNamesToRanksAndFlips[i[otherIndex]]
otherPos = otherFlip * abs(blocks[0][otherIndex] +
blocks[-1][otherIndex] + blocks[-1][2])
numOfAlignedLetterPairs = sum(i[2] for i in blocks)
yield i[seqIndex], otherRank, otherPos, numOfAlignedLetterPairs
def mySortedRanges(seqRanges, sortOpt, seqIndex, alignments, otherRanges):
rangesGroupedBySeqName = itertools.groupby(seqRanges, itemgetter(0))
g = [list(ranges) for seqName, ranges in rangesGroupedBySeqName]
for i in g:
if i[0][3] > 1:
i.reverse()
if sortOpt == "1":
g.sort(key=nameKey)
if sortOpt == "2":
g.sort(key=sizeKey)
if sortOpt == "3":
otherNamesToRanksAndFlips = dict(rankAndFlipPerSeq(otherRanges))
alns = sorted(alignmentSortData(alignments, seqIndex,
otherNamesToRanksAndFlips))
alnsGroupedBySeqName = itertools.groupby(alns, itemgetter(0))
seqNamesToLists = dict((k, list(v)) for k, v in alnsGroupedBySeqName)
g.sort(key=functools.partial(alignmentKey, seqNamesToLists))
return [j for i in g for j in i]
def allSortedRanges(opts, alignments, alignmentsB,
seqRanges1, seqRangesB1, seqRanges2, seqRangesB2):
o1, oB1 = twoValuesFromOption(opts.strands1, ":")
o2, oB2 = twoValuesFromOption(opts.strands2, ":")
if o1 == "1" and o2 == "1":
raise Exception("the strand options have circular dependency")
seqRanges1 = list(rangesWithStrandInfo(seqRanges1, o1, alignments, 0))
seqRanges2 = list(rangesWithStrandInfo(seqRanges2, o2, alignments, 1))
seqRangesB1 = list(rangesWithStrandInfo(seqRangesB1, oB1, alignmentsB, 0))
seqRangesB2 = list(rangesWithStrandInfo(seqRangesB2, oB2, alignmentsB, 1))
o1, oB1 = twoValuesFromOption(opts.sort1, ":")
o2, oB2 = twoValuesFromOption(opts.sort2, ":")
if o1 == "3" and o2 == "3":
raise Exception("the sort options have circular dependency")
if o1 != "3":
s1 = mySortedRanges(seqRanges1, o1, None, None, None)
if o2 != "3":
s2 = mySortedRanges(seqRanges2, o2, None, None, None)
if o1 == "3":
s1 = mySortedRanges(seqRanges1, o1, 0, alignments, s2)
if o2 == "3":
s2 = mySortedRanges(seqRanges2, o2, 1, alignments, s1)
t1 = mySortedRanges(seqRangesB1, oB1, 0, alignmentsB, s2)
t2 = mySortedRanges(seqRangesB2, oB2, 1, alignmentsB, s1)
return s1 + t1, s2 + t2
def prettyNum(n):
t = str(n)
groups = []
while t:
groups.append(t[-3:])
t = t[:-3]
return ",".join(reversed(groups))
def sizeText(size):
suffixes = "bp", "kb", "Mb", "Gb"
for i, x in enumerate(suffixes):
j = 10 ** (i * 3)
if size < j * 10:
return "%.2g" % (1.0 * size / j) + x
if size < j * 1000 or i == len(suffixes) - 1:
return "%.0f" % (1.0 * size / j) + x
def labelText(seqRange, labelOpt):
seqName, beg, end, strandNum = seqRange
if labelOpt == 1:
return seqName + ": " + sizeText(end - beg)
if labelOpt == 2:
return seqName + ":" + prettyNum(beg) + ": " + sizeText(end - beg)
if labelOpt == 3:
return seqName + ":" + prettyNum(beg) + "-" + prettyNum(end)
return seqName
def rangeLabels(seqRanges, labelOpt, font, fontsize, image_mode, textRot):
if fontsize:
image_size = 1, 1
im = Image.new(image_mode, image_size)
draw = ImageDraw.Draw(im)
x = y = 0
for r in seqRanges:
text = labelText(r, labelOpt)
if fontsize:
x, y = draw.textsize(text, font=font)
if textRot:
x, y = y, x
yield text, x, y, r[3]
def dataFromRanges(sortedRanges, font, fontSize, imageMode, labelOpt, textRot):
for seqName, rangeBeg, rangeEnd, strandNum in sortedRanges:
out = [seqName, str(rangeBeg), str(rangeEnd)]
if strandNum > 0:
out.append(".+-"[strandNum])
warn("\t".join(out))
warn("")
rangeSizes = [e - b for n, b, e, s in sortedRanges]
labs = list(rangeLabels(sortedRanges, labelOpt, font, fontSize,
imageMode, textRot))
margin = max(i[2] for i in labs)
# xxx the margin may be too big, because some labels may get omitted
return rangeSizes, labs, margin
def div_ceil(x, y):
'''Return x / y rounded up.'''
q, r = divmod(x, y)
return q + (r != 0)
def get_bp_per_pix(rangeSizes, pixTweenRanges, maxPixels):
'''Get the minimum bp-per-pixel that fits in the size limit.'''
warn("choosing bp per pixel...")
numOfRanges = len(rangeSizes)
maxPixelsInRanges = maxPixels - pixTweenRanges * (numOfRanges - 1)
if maxPixelsInRanges < numOfRanges:
raise Exception("can't fit the image: too many sequences?")
negLimit = -maxPixelsInRanges
negBpPerPix = sum(rangeSizes) // negLimit
while True:
if sum(i // negBpPerPix for i in rangeSizes) >= negLimit:
return -negBpPerPix
negBpPerPix -= 1
def getRangePixBegs(rangePixLens, pixTweenRanges, margin):
'''Get the start pixel for each range.'''
rangePixBegs = []
pix_tot = margin - pixTweenRanges
for i in rangePixLens:
pix_tot += pixTweenRanges
rangePixBegs.append(pix_tot)
pix_tot += i
return rangePixBegs
def pixelData(rangeSizes, bp_per_pix, pixTweenRanges, margin):
'''Return pixel information about the ranges.'''
rangePixLens = [div_ceil(i, bp_per_pix) for i in rangeSizes]
rangePixBegs = getRangePixBegs(rangePixLens, pixTweenRanges, margin)
tot_pix = rangePixBegs[-1] + rangePixLens[-1]
return rangePixBegs, rangePixLens, tot_pix
def drawLineForward(hits, width, bp_per_pix, beg1, beg2, size):
while True:
q1, r1 = divmod(beg1, bp_per_pix)
q2, r2 = divmod(beg2, bp_per_pix)
hits[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, beg1, beg2, size):
while True:
q1, r1 = divmod(beg1, bp_per_pix)
q2, r2 = divmod(beg2, bp_per_pix)
hits[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 strandAndOrigin(ranges, beg, size):
isReverseStrand = (beg < 0)
if isReverseStrand:
beg = -(beg + size)
for rangeBeg, rangeEnd, isReverseRange, origin in ranges:
if rangeEnd > beg: # assumes the ranges are sorted
return (isReverseStrand != isReverseRange), origin
def alignmentPixels(width, height, alignments, bp_per_pix,
rangeDict1, rangeDict2):
hits = [0] * (width * height) # the image data
for seq1, seq2, blocks in alignments:
beg1, beg2, size = blocks[0]
isReverse1, ori1 = strandAndOrigin(rangeDict1[seq1], beg1, size)
isReverse2, ori2 = strandAndOrigin(rangeDict2[seq2], beg2, size)
for beg1, beg2, size in blocks:
if isReverse1:
beg1 = -(beg1 + size)
beg2 = -(beg2 + size)
if isReverse1 == isReverse2:
drawLineForward(hits, width, bp_per_pix,
ori1 + beg1, ori2 + beg2, size)
else:
drawLineReverse(hits, width, bp_per_pix,
ori1 + beg1, ori2 - beg2 - 1, size)
return hits
def expandedSeqDict(seqDict):
'''Allow lookup by short sequence names, e.g. chr7 as well as hg19.chr7.'''
newDict = seqDict.copy()
for name, x in seqDict.items():
if "." in name:
base = name.split(".")[-1]
if base in newDict: # an ambiguous case was found:
return seqDict # so give up completely
newDict[base] = x
return newDict
def readBed(fileName, rangeDict):
for line in myOpen(fileName):
w = line.split()
if not w: continue
seqName = w[0]
if seqName not in rangeDict: continue
beg = int(w[1])
end = int(w[2])
layer = 900
color = "#fbf"
if len(w) > 4:
if w[4] != ".":
layer = float(w[4])
if len(w) > 5:
if len(w) > 8 and w[8].count(",") == 2:
color = "rgb(" + w[8] + ")"
else:
strand = w[5]
isRev = rangeDict[seqName][0][2]
if strand == "+" and not isRev or strand == "-" and isRev:
color = "#ffe8e8"
if strand == "-" and not isRev or strand == "+" and isRev:
color = "#e8e8ff"
yield layer, color, seqName, beg, end
def commaSeparatedInts(text):
return map(int, text.rstrip(",").split(","))
def readGenePred(opts, fileName, rangeDict):
for line in myOpen(fileName):
fields = line.split()
if not fields: continue
if fields[2] not in "+-": fields = fields[1:]
seqName = fields[1]
if seqName not in rangeDict: continue
#strand = fields[2]
cdsBeg = int(fields[5])
cdsEnd = int(fields[6])
exonBegs = commaSeparatedInts(fields[8])
exonEnds = commaSeparatedInts(fields[9])
for beg, end in zip(exonBegs, exonEnds):
yield 300, opts.exon_color, seqName, beg, end
b = max(beg, cdsBeg)
e = min(end, cdsEnd)
if b < e: yield 400, opts.cds_color, seqName, b, e
def readRmsk(fileName, rangeDict):
for line in myOpen(fileName):
fields = line.split()
if len(fields) == 17: # rmsk.txt
seqName = fields[5]
if seqName not in rangeDict: continue # do this ASAP for speed
beg = int(fields[6])
end = int(fields[7])
strand = fields[9]
repeatClass = fields[11]
elif len(fields) == 15: # .out
seqName = fields[4]
if seqName not in rangeDict: continue
beg = int(fields[5]) - 1
end = int(fields[6])
strand = fields[8]
repeatClass = fields[10]
else:
continue
if repeatClass in ("Low_complexity", "Simple_repeat"):
yield 200, "#fbf", seqName, beg, end
elif (strand == "+") != rangeDict[seqName][0][2]:
yield 100, "#ffe8e8", seqName, beg, end
else:
yield 100, "#e8e8ff", seqName, beg, end
def isExtraFirstGapField(fields):
return fields[4].isdigit()
def readGaps(opts, fileName, rangeDict):
'''Read locations of unsequenced gaps, from an agp or gap file.'''
for line in myOpen(fileName):
w = line.split()
if not w or w[0][0] == "#": continue
if isExtraFirstGapField(w): w = w[1:]
if w[4] not in "NU": continue
seqName = w[0]
if seqName not in rangeDict: continue
end = int(w[2])
beg = end - int(w[5]) # zero-based coordinate
if w[7] == "yes":
yield 3000, opts.bridged_color, seqName, beg, end
else:
yield 2000, opts.unbridged_color, seqName, beg, end
def bedBoxes(beds, rangeDict, margin, edge, isTop, bpPerPix):
for layer, color, seqName, bedBeg, bedEnd in beds:
for rangeBeg, rangeEnd, isReverseRange, origin in rangeDict[seqName]:
beg = max(bedBeg, rangeBeg)
end = min(bedEnd, rangeEnd)
if beg >= end: continue
if isReverseRange:
beg, end = -end, -beg
if layer <= 1000:
# include partly-covered pixels
b = (origin + beg) // bpPerPix
e = div_ceil(origin + end, bpPerPix)
else:
# exclude partly-covered pixels
b = div_ceil(origin + beg, bpPerPix)
e = (origin + end) // bpPerPix
if e <= b: continue
if bedEnd >= rangeEnd: # include partly-covered end pixels
if isReverseRange:
b = (origin + beg) // bpPerPix
else:
e = div_ceil(origin + end, bpPerPix)
if isTop:
box = b, margin, e, edge
else:
box = margin, b, edge, e
yield layer, color, box
def drawAnnotations(im, boxes):
# xxx use partial transparency for different-color overlaps?
for layer, color, box in boxes:
im.paste(color, box)
def placedLabels(labels, rangePixBegs, rangePixLens, beg, end):
'''Return axis labels with endpoint & sort-order information.'''
maxWidth = end - beg
for i, j, k in zip(labels, rangePixBegs, rangePixLens):
text, textWidth, textHeight, strandNum = i
if textWidth > maxWidth:
continue
labelBeg = j + (k - textWidth) // 2
labelEnd = labelBeg + textWidth
sortKey = textWidth - k
if labelBeg < beg:
sortKey += maxWidth * (beg - labelBeg)
labelBeg = beg
labelEnd = beg + textWidth
if labelEnd > end:
sortKey += maxWidth * (labelEnd - end)
labelEnd = end
labelBeg = end - textWidth
yield sortKey, labelBeg, labelEnd, text, textHeight, strandNum
def nonoverlappingLabels(labels, minPixTweenLabels):
'''Get a subset of non-overlapping axis labels, greedily.'''
out = []
for i in labels:
beg = i[1] - minPixTweenLabels
end = i[2] + minPixTweenLabels
if all(j[2] <= beg or j[1] >= end for j in out):
out.append(i)
return out
def axisImage(labels, rangePixBegs, rangePixLens, textRot,
textAln, font, image_mode, opts):
'''Make an image of axis labels.'''
beg = rangePixBegs[0]
end = rangePixBegs[-1] + rangePixLens[-1]
margin = max(i[2] for i in labels)
labels = sorted(placedLabels(labels, rangePixBegs, rangePixLens, beg, end))
minPixTweenLabels = 0 if textRot else opts.label_space
labels = nonoverlappingLabels(labels, minPixTweenLabels)
image_size = (margin, end) if textRot else (end, margin)
im = Image.new(image_mode, image_size, opts.margin_color)
draw = ImageDraw.Draw(im)
for sortKey, labelBeg, labelEnd, text, textHeight, strandNum in labels:
base = margin - textHeight if textAln else 0
position = (base, labelBeg) if textRot else (labelBeg, base)
fill = ("black", opts.forwardcolor, opts.reversecolor)[strandNum]
draw.text(position, text, font=font, fill=fill)
return im
def rangesWithOrigins(sortedRanges, rangePixBegs, rangePixLens, bpPerPix):
for i, j, k in zip(sortedRanges, rangePixBegs, rangePixLens):
seqName, rangeBeg, rangeEnd, strandNum = i
isReverseRange = (strandNum > 1)
if isReverseRange:
origin = bpPerPix * (j + k) + rangeBeg
else:
origin = bpPerPix * j - rangeBeg
yield seqName, (rangeBeg, rangeEnd, isReverseRange, origin)
def rangesPerSeq(sortedRanges, rangePixBegs, rangePixLens, bpPerPix):
a = rangesWithOrigins(sortedRanges, rangePixBegs, rangePixLens, bpPerPix)
for k, v in itertools.groupby(a, itemgetter(0)):
yield k, sorted(i[1] for i in v)
def getFont(opts):
if opts.fontfile:
return ImageFont.truetype(opts.fontfile, opts.fontsize)
fileNames = []
try:
x = ["fc-match", "-f%{file}", "arial"]
p = subprocess.Popen(x, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
out, err = p.communicate()
fileNames.append(out)
except OSError as e:
warn("fc-match error: " + str(e))
fileNames.append("/Library/Fonts/Arial.ttf") # for Mac
for i in fileNames:
try:
font = ImageFont.truetype(i, opts.fontsize)
warn("font: " + i)
return font
except IOError as e:
warn("font load error: " + str(e))
return ImageFont.load_default()
def lastDotplot(opts, args):
font = getFont(opts)
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])
maxGap1, maxGapB1 = twoValuesFromOption(opts.max_gap1, ":")
maxGap2, maxGapB2 = twoValuesFromOption(opts.max_gap2, ":")
warn("reading alignments...")
alnData = readAlignments(args[0], opts)
alignments, seqRanges1, coverDict1, seqRanges2, coverDict2 = alnData
if not alignments: raise Exception("there are no alignments")
warn("cutting...")
coverDict1 = dict(mergedRangesPerSeq(coverDict1))
coverDict2 = dict(mergedRangesPerSeq(coverDict2))
minAlignedBases = min(coveredLength(coverDict1), coveredLength(coverDict2))
pad = int(opts.pad * minAlignedBases)
cutRanges1 = list(trimmed(seqRanges1, coverDict1, minAlignedBases,
maxGap1, pad, pad))
cutRanges2 = list(trimmed(seqRanges2, coverDict2, minAlignedBases,
maxGap2, pad, pad))
warn("reading secondary alignments...")
alnDataB = readSecondaryAlignments(opts, cutRanges1, cutRanges2)
alignmentsB, seqRangesB1, coverDictB1, seqRangesB2, coverDictB2 = alnDataB
warn("cutting...")
coverDictB1 = dict(mergedRangesPerSeq(coverDictB1))
coverDictB2 = dict(mergedRangesPerSeq(coverDictB2))
cutRangesB1 = trimmed(seqRangesB1, coverDictB1, minAlignedBases,
maxGapB1, 0, 0)
cutRangesB2 = trimmed(seqRangesB2, coverDictB2, minAlignedBases,
maxGapB2, 0, 0)
warn("sorting...")
sortOut = allSortedRanges(opts, alignments, alignmentsB,
cutRanges1, cutRangesB1, cutRanges2, cutRangesB2)
sortedRanges1, sortedRanges2 = sortOut
textRot1 = "vertical".startswith(opts.rot1)
i1 = dataFromRanges(sortedRanges1, font,
opts.fontsize, image_mode, opts.labels1, textRot1)
rangeSizes1, labelData1, tMargin = i1
textRot2 = "horizontal".startswith(opts.rot2)
i2 = dataFromRanges(sortedRanges2, font,
opts.fontsize, image_mode, opts.labels2, textRot2)
rangeSizes2, labelData2, lMargin = i2
maxPixels1 = opts.width - lMargin
maxPixels2 = opts.height - tMargin
bpPerPix1 = get_bp_per_pix(rangeSizes1, opts.border_pixels, maxPixels1)
bpPerPix2 = get_bp_per_pix(rangeSizes2, opts.border_pixels, maxPixels2)
bpPerPix = max(bpPerPix1, bpPerPix2)
warn("bp per pixel = " + str(bpPerPix))
p1 = pixelData(rangeSizes1, bpPerPix, opts.border_pixels, lMargin)
rangePixBegs1, rangePixLens1, width = p1
rangeDict1 = dict(rangesPerSeq(sortedRanges1, rangePixBegs1,
rangePixLens1, bpPerPix))
p2 = pixelData(rangeSizes2, bpPerPix, opts.border_pixels, tMargin)
rangePixBegs2, rangePixLens2, height = p2
rangeDict2 = dict(rangesPerSeq(sortedRanges2, rangePixBegs2,
rangePixLens2, bpPerPix))
warn("width: " + str(width))
warn("height: " + str(height))
warn("processing alignments...")
hits = alignmentPixels(width, height, alignments + alignmentsB, bpPerPix,
rangeDict1, rangeDict2)
warn("reading annotations...")
rangeDict1 = expandedSeqDict(rangeDict1)
beds1 = itertools.chain(readBed(opts.bed1, rangeDict1),
readRmsk(opts.rmsk1, rangeDict1),
readGenePred(opts, opts.genePred1, rangeDict1),
readGaps(opts, opts.gap1, rangeDict1))
b1 = bedBoxes(beds1, rangeDict1, tMargin, height, True, bpPerPix)
rangeDict2 = expandedSeqDict(rangeDict2)
beds2 = itertools.chain(readBed(opts.bed2, rangeDict2),
readRmsk(opts.rmsk2, rangeDict2),
readGenePred(opts, opts.genePred2, rangeDict2),
readGaps(opts, opts.gap2, rangeDict2))
b2 = bedBoxes(beds2, rangeDict2, lMargin, width, False, bpPerPix)
boxes = sorted(itertools.chain(b1, b2))
warn("drawing...")
image_size = width, height
im = Image.new(image_mode, image_size, opts.background_color)
drawAnnotations(im, boxes)
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 = axisImage(labelData1, rangePixBegs1, rangePixLens1,
textRot1, False, font, image_mode, opts)
if textRot1:
axis1 = axis1.transpose(Image.ROTATE_90)
axis2 = axisImage(labelData2, rangePixBegs2, rangePixLens2,
textRot2, textRot2, font, image_mode, opts)
if not textRot2:
axis2 = axis2.transpose(Image.ROTATE_270)
im.paste(axis1, (0, 0))
im.paste(axis2, (0, 0))
for i in rangePixBegs1[1:]:
box = i - opts.border_pixels, tMargin, i, height
im.paste(opts.border_color, box)
for i in rangePixBegs2[1:]:
box = lMargin, i - opts.border_pixels, width, i
im.paste(opts.border_color, box)
im.save(args[1])
if __name__ == "__main__":
usage = """%prog --help
or: %prog [options] maf-or-tab-alignments dotplot.png
or: %prog [options] maf-or-tab-alignments dotplot.gif
or: ..."""
description = "Draw a dotplot of pair-wise sequence alignments in MAF or tabular format."
op = optparse.OptionParser(usage=usage, description=description)
op.add_option("-v", "--verbose", action="count",
help="show progress messages & data about the plot")
op.add_option("-1", "--seq1", metavar="PATTERN", action="append",
default=[],
help="which sequences to show from the 1st genome")
op.add_option("-2", "--seq2", metavar="PATTERN", action="append",
default=[],
help="which sequences to show from the 2nd genome")
# 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("-c", "--forwardcolor", metavar="COLOR", default="red",
help="color for forward alignments (default: %default)")
op.add_option("-r", "--reversecolor", metavar="COLOR", default="blue",
help="color for reverse alignments (default: %default)")
op.add_option("--alignments", metavar="FILE", help="secondary alignments")
op.add_option("--sort1", default="1", metavar="N",
help="genome1 sequence order: 0=input order, 1=name order, "
"2=length order, 3=alignment order (default=%default)")
op.add_option("--sort2", default="1", metavar="N",
help="genome2 sequence order: 0=input order, 1=name order, "
"2=length order, 3=alignment order (default=%default)")
op.add_option("--strands1", default="0", metavar="N", help=
"genome1 sequence orientation: 0=forward orientation, "
"1=alignment orientation (default=%default)")
op.add_option("--strands2", default="0", metavar="N", help=
"genome2 sequence orientation: 0=forward orientation, "
"1=alignment orientation (default=%default)")
op.add_option("--max-gap1", metavar="FRAC", default="0.5,2", help=
"maximum unaligned (end,mid) gap in genome1: "
"fraction of aligned length (default=%default)")
op.add_option("--max-gap2", metavar="FRAC", default="0.5,2", help=
"maximum unaligned (end,mid) gap in genome2: "
"fraction of aligned length (default=%default)")
op.add_option("--pad", metavar="FRAC", type="float", default=0.04, help=
"pad length when cutting unaligned gaps: "
"fraction of aligned length (default=%default)")
op.add_option("--border-pixels", metavar="INT", type="int", default=1,
help="number of pixels between sequences (default=%default)")
op.add_option("--border-color", metavar="COLOR", default="black",
help="color for pixels between sequences (default=%default)")
# --break-color and/or --break-pixels for intra-sequence breaks?
op.add_option("--margin-color", metavar="COLOR", default="#dcdcdc",
help="margin color")
og = optparse.OptionGroup(op, "Text options")
og.add_option("-f", "--fontfile", metavar="FILE",
help="TrueType or OpenType font file")
og.add_option("-s", "--fontsize", metavar="SIZE", type="int", default=14,
help="TrueType or OpenType font size (default: %default)")
og.add_option("--labels1", type="int", default=0, metavar="N", help=
"genome1 labels: 0=name, 1=name:length, "
"2=name:start:length, 3=name:start-end (default=%default)")
og.add_option("--labels2", type="int", default=0, metavar="N", help=
"genome2 labels: 0=name, 1=name:length, "
"2=name:start:length, 3=name:start-end (default=%default)")
og.add_option("--rot1", metavar="ROT", default="h",
help="text rotation for the 1st genome (default=%default)")
og.add_option("--rot2", metavar="ROT", default="v",
help="text rotation for the 2nd genome (default=%default)")
op.add_option_group(og)
og = optparse.OptionGroup(op, "Annotation options")
og.add_option("--bed1", metavar="FILE",
help="read genome1 annotations from BED file")
og.add_option("--bed2", metavar="FILE",
help="read genome2 annotations from BED file")
og.add_option("--rmsk1", metavar="FILE", help="read genome1 repeats from "
"RepeatMasker .out or rmsk.txt file")
og.add_option("--rmsk2", metavar="FILE", help="read genome2 repeats from "
"RepeatMasker .out or rmsk.txt file")
op.add_option_group(og)
og = optparse.OptionGroup(op, "Gene options")
og.add_option("--genePred1", metavar="FILE",
help="read genome1 genes from genePred file")
og.add_option("--genePred2", metavar="FILE",
help="read genome2 genes from genePred file")
og.add_option("--exon-color", metavar="COLOR", default="PaleGreen",
help="color for exons (default=%default)")
og.add_option("--cds-color", metavar="COLOR", default="LimeGreen",
help="color for protein-coding regions (default=%default)")
op.add_option_group(og)
og = optparse.OptionGroup(op, "Unsequenced gap options")
og.add_option("--gap1", metavar="FILE",
help="read genome1 unsequenced gaps from agp or gap file")
og.add_option("--gap2", metavar="FILE",
help="read genome2 unsequenced gaps from agp or gap file")
og.add_option("--bridged-color", metavar="COLOR", default="yellow",
help="color for bridged gaps (default: %default)")
og.add_option("--unbridged-color", metavar="COLOR", default="orange",
help="color for unbridged gaps (default: %default)")
op.add_option_group(og)
(opts, args) = op.parse_args()
if len(args) != 2: op.error("2 arguments needed")
opts.background_color = "white"
opts.label_space = 5 # minimum number of pixels between axis labels
try: lastDotplot(opts, args)
except KeyboardInterrupt: pass # avoid silly error message
except Exception as e:
prog = os.path.basename(sys.argv[0])
sys.exit(prog + ": error: " + str(e))