/usr/bin/maf-join is in last-align 921-1.
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# Copyright 2009, 2010, 2011 Martin C. Frith
# Join two or more sets of MAF-format multiple alignments into bigger
# multiple alignments. The 'join field' is the top genome, which
# should be the same for each input. Each input should be sorted by
# position in the top genome.
# WARNING: Alignment columns with a gap in the top genome are joined
# arbitrarily!!!
import sys, os, fileinput, optparse, signal
signal.signal(signal.SIGPIPE, signal.SIG_DFL) # stop spurious error message
class peekable: # Adapted from Python Cookbook 2nd edition
"""An iterator that supports a peek operation."""
def __init__(self, iterable):
self.it = iter(iterable)
self.cache = []
def __iter__(self):
return self
def next(self):
if self.cache: return self.cache.pop()
else: return self.it.next()
def peek(self):
if not self.cache: self.cache.append(self.it.next())
return self.cache[0]
def maxLen(things): return max(map(len, things))
class MafBlock:
def __init__(self, chr, beg, end, strand, chrSize, seq, prob):
self.chr = chr # chromosome names
self.beg = beg # alignment begin coordinates
self.end = end # alignment end coordinates
self.strand = strand
self.chrSize = chrSize # chromosome sizes
self.seq = seq # aligned sequences, including gaps
self.prob = prob # probabilities (may be empty)
def __nonzero__(self):
return len(self.seq) > 0
def __cmp__(self, other):
return cmp(self.chr[:1] + self.beg[:1], other.chr[:1] + other.beg[:1])
def before(self, other):
return (self.chr[0], self.end[0]) <= (other.chr[0], other.beg[0])
def after(self, other):
return (self.chr[0], self.beg[0]) >= (other.chr[0], other.end[0])
def addLine(self, line):
words = line.split()
if line.startswith('s'):
self.chr.append(words[1])
self.beg.append(int(words[2]))
self.end.append(int(words[2]) + int(words[3]))
self.strand.append(words[4])
self.chrSize.append(words[5])
self.seq.append(list(words[6]))
elif line.startswith('p'):
self.prob.append(words[1])
def write(self):
beg = map(str, self.beg)
size = [str(e-b) for b, e in zip(self.beg, self.end)]
seq = [''.join(i) for i in self.seq]
columns = self.chr, beg, size, self.strand, self.chrSize, seq
widths = map(maxLen, columns)
print 'a'
for row in zip(*columns):
widthsAndFields = zip(widths, row)
field0 = "%-*s" % widthsAndFields[0] # left-justify
fields = ["%*s" % i for i in widthsAndFields[1:]] # right-justify
print 's', field0, ' '.join(fields)
pad = ' '.join(' ' * i for i in widths[:-1])
for i in self.prob:
print 'p', pad, i
print # blank line afterwards
def topSeqBeg(maf): return maf.beg[0]
def topSeqEnd(maf): return maf.end[0]
def emptyMaf(): return MafBlock([], [], [], [], [], [], [])
def joinOnFirstItem(x, y):
if x[0] != y[0]:
raise ValueError('join fields not equal:\n'+str(x[0])+'\n'+str(y[0]))
return x + y[1:]
def mafEasyJoin(x, y):
'''Join two MAF blocks on the top sequence.'''
xJoin = zip(x.chr, x.beg, x.end, x.strand, x.chrSize, x.seq)
yJoin = zip(y.chr, y.beg, y.end, y.strand, y.chrSize, y.seq)
joined = joinOnFirstItem(xJoin, yJoin)
chr, beg, end, strand, chrSize, seq = zip(*joined)
prob = x.prob + y.prob
return MafBlock(chr, beg, end, strand, chrSize, seq, prob)
def countNonGaps(s): return len(s) - s.count('-')
def nthNonGap(s, n):
'''Get the start position of the n-th non-gap.'''
for i, x in enumerate(s):
if x != '-':
if n == 0: return i
n -= 1
raise ValueError('non-gap not found')
def nthLastNonGap(s, n):
'''Get the end position of the n-th last non-gap.'''
return len(s) - nthNonGap(s[::-1], n)
def mafSlice(maf, alnBeg, alnEnd):
'''Return a slice of a MAF block, using coordinates in the alignment.'''
beg = [b + countNonGaps(s[:alnBeg]) for b, s in zip(maf.beg, maf.seq)]
end = [e - countNonGaps(s[alnEnd:]) for e, s in zip(maf.end, maf.seq)]
seq = [i[alnBeg:alnEnd] for i in maf.seq]
prob = [i[alnBeg:alnEnd] for i in maf.prob]
return MafBlock(maf.chr, beg, end, maf.strand, maf.chrSize, seq, prob)
def mafSliceTopSeq(maf, newTopSeqBeg, newTopSeqEnd):
'''Return a slice of a MAF block, using coordinates in the top sequence.'''
lettersFromBeg = newTopSeqBeg - topSeqBeg(maf)
lettersFromEnd = topSeqEnd(maf) - newTopSeqEnd
alnBeg = nthNonGap(maf.seq[0], lettersFromBeg)
alnEnd = nthLastNonGap(maf.seq[0], lettersFromEnd)
return mafSlice(maf, alnBeg, alnEnd)
def jumpGaps(sequence, index):
'''Return the next index of the sequence where there is a non-gap.'''
nextIndex = index
while sequence[nextIndex] == '-': nextIndex += 1
return nextIndex
def gapsToAdd(sequences):
'''Return new gaps and their positions, needed to align the non-gaps.'''
gapInfo = [[] for i in sequences]
gapBeg = [0 for i in sequences]
try:
while True:
gapEnd = [jumpGaps(s, p) for s, p in zip(sequences, gapBeg)]
gapSize = [e-b for b, e in zip(gapBeg, gapEnd)]
maxGapSize = max(gapSize)
for s, e, i in zip(gapSize, gapEnd, gapInfo):
if s < maxGapSize:
newGap = maxGapSize - s
i.append((newGap, e))
gapBeg = [e+1 for e in gapEnd]
except IndexError: return gapInfo
def chunksAndGaps(s, gapsAndPositions, oneGap):
'''Yield chunks of "s" interspersed with gaps at given positions.'''
oldPosition = 0
for gapLen, position in gapsAndPositions:
yield s[oldPosition:position]
yield oneGap * gapLen
oldPosition = position
yield s[oldPosition:]
def mafAddGaps(maf, gapsAndPositions):
'''Add the given gaps at the given positions to a MAF block.'''
maf.seq = [sum(chunksAndGaps(i, gapsAndPositions, ['-']), [])
for i in maf.seq]
maf.prob = [''.join(chunksAndGaps(i, gapsAndPositions, '~'))
for i in maf.prob]
def mafJoin(mafs):
'''Intersect and join overlapping MAF blocks.'''
newTopSeqBeg = max(map(topSeqBeg, mafs))
newTopSeqEnd = min(map(topSeqEnd, mafs))
mafs = [mafSliceTopSeq(i, newTopSeqBeg, newTopSeqEnd) for i in mafs]
topSeqs = [i.seq[0] for i in mafs]
gapInfo = gapsToAdd(topSeqs)
for maf, gapsAndPositions in zip(mafs, gapInfo):
mafAddGaps(maf, gapsAndPositions)
return reduce(mafEasyJoin, mafs)
def mafInput(lines):
'''Read lines and yield MAF blocks.'''
maf = emptyMaf()
for line in lines:
if line.isspace():
if maf: yield maf
maf = emptyMaf()
else:
maf.addLine(line)
if maf: yield maf
def sortedMafInput(lines):
'''Read lines and yield MAF blocks, checking that they are in order.'''
old = emptyMaf()
for maf in mafInput(lines):
if maf < old: sys.exit(progName + ": MAF blocks not sorted properly")
yield maf
old = maf
def allOverlaps(sequences, beg, end):
'''Yield all combinations of MAF blocks that overlap in the top genome.'''
assert beg < end
if not sequences:
yield ()
return
for i in sequences[0]:
if topSeqEnd(i) <= beg: continue
if topSeqBeg(i) >= end: break # assumes they're sorted by position
newBeg = max(beg, topSeqBeg(i))
newEnd = min(end, topSeqEnd(i))
for j in allOverlaps(sequences[1:], newBeg, newEnd):
yield (i,) + j
def nextWindow(window, input, referenceMaf):
'''Yield "relevant" MAF blocks, based on overlap with referenceMaf.'''
for maf in window:
if not maf.before(referenceMaf): yield maf
try:
while True:
maf = input.peek()
if maf.after(referenceMaf): break
maf = input.next()
if not maf.before(referenceMaf): yield maf
except StopIteration: pass
def overlappingMafs(sortedMafInputs):
'''Yield all combinations of MAF blocks that overlap in the top genome.'''
if not sortedMafInputs: return
head, tail = sortedMafInputs[0], sortedMafInputs[1:]
windows = [[] for t in tail]
for h in head: # iterate over MAF blocks in the first input
windows = [list(nextWindow(w, t, h)) for w, t in zip(windows, tail)]
for i in allOverlaps(windows, topSeqBeg(h), topSeqEnd(h)):
yield (h,) + i
op = optparse.OptionParser(usage="%prog sorted-file1.maf sorted-file2.maf ...")
(opts, args) = op.parse_args()
progName = os.path.basename(sys.argv[0])
inputs = [peekable(sortedMafInput(fileinput.input(i))) for i in args]
for mafs in overlappingMafs(inputs):
mafJoin(mafs).write()
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