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#! /usr/bin/env python
# Copyright 2009, 2010 Martin C. Frith
# Read MAF-format sequence alignments: write them in human-friendly
# HTML, with colours indicating alignment probabilities (from MAF
# lines starting with 'p'.)
import fileinput, operator, itertools, optparse, signal
signal.signal(signal.SIGPIPE, signal.SIG_DFL) # stop spurious error message
op = optparse.OptionParser(usage="%prog [options] my-alignments.maf")
op.add_option('-l', '--linesize', type="int", default=100, metavar="CHARS",
help="write CHARS characters per line (default: %default)")
(opts, args) = op.parse_args()
if opts.linesize <= 0: op.error("option -l: should be >= 1")
print '''
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
"http://www.w3.org/TR/html4/strict.dtd">
<html lang="en"><head>
<meta http-equiv="Content-type" content="text/html; charset=UTF-8">
<title>Reliable Alignments</title>
<style type="text/css">
.a {background-color: #3333FF}
.b {background-color: #9933FF}
.c {background-color: #FF66CC}
.d {background-color: #FF3333}
.e {background-color: #FF9933}
.f {background-color: #FFFF00}
</style>
</head><body>
'''
print '''
<div style="line-height:1">
<pre style="display:inline; margin-right:2em"><span class="a"> </span> prob > 0.999</pre>
<pre style="display:inline; margin-right:2em"><span class="b"> </span> prob > 0.99 </pre>
<pre style="display:inline; margin-right:2em"><span class="c"> </span> prob > 0.95 </pre>
<pre style="display:inline; margin-right:2em"><span class="d"> </span> prob > 0.9 </pre>
<pre style="display:inline; margin-right:2em"><span class="e"> </span> prob > 0.5 </pre>
<pre style="display:inline; margin-right:2em"><span class="f"> </span> prob ≤ 0.5 </pre>
</div>
'''
def mafInput(lines):
'''Read lines and yield MAF blocks.'''
maf = []
for line in lines:
if line.startswith('#'): continue
if line.isspace():
if maf: yield maf
maf = []
else:
maf.append(line.split())
if maf: yield maf
def columnSymbol(column):
'''Return a star if all the letters are identical, or else a space.'''
firstSymbol = column[0].lower()
for i in column[1:]:
if i.lower() != firstSymbol: return ' '
return '*'
def probabilityClass(probabilityColumn):
# here, imap seems to be a little bit faster than map:
try: p = reduce(operator.mul, itertools.imap(float, probabilityColumn))
except ValueError: return None
if p > 0.999: return 'a'
elif p > 0.99: return 'b'
elif p > 0.95: return 'c'
elif p > 0.9: return 'd'
elif p > 0.5: return 'e'
else: return 'f'
def identicalRuns(s): # I want to use groupby, but it's new in python 2.4
'''Yield (start, end, item) for each run of identical items in s.'''
for i, x in enumerate(s):
if not i or x != old:
if i: yield start, i, old
start = i
old = x
if s: yield start, i+1, x
def htmlSpans(text, spans):
for beg, end, key in spans:
chunk = text[beg:end]
if key: yield '<span class="%s">%s</span>' % (key, chunk)
else: yield chunk
def cunningCoordinate(sLine):
'''Parse a MAF start coordinate, dealing cunningly with reverse strands.'''
coordinate = int(sLine[1])
if sLine[3] == '+': return coordinate
else: return coordinate - int(sLine[4]) - 1
def coordinateString(coordinate): return str(abs(coordinate))
def maxlen(s): return max(map(len, s))
def countOfNonGaps(s): return len(s) - s.count('-')
for maf in mafInput(fileinput.input(args)):
aLines = [i[1:] for i in maf if i[0] == 'a'] # there should be 1 'a' line
scores = [i for i in aLines[0] if i.startswith('score=')]
if scores: print '<h3>Alignment %s:</h3>' % scores[0]
else: print '<h3>Alignment:</h3>'
sLines = [i[1:] for i in maf if i[0] == 's']
names = [i[0] for i in sLines]
nameWidth = maxlen(names)
coordinates = map(cunningCoordinate, sLines)
sequences = [i[5] for i in sLines]
alignmentLength = maxlen(sequences) # ?
pLines = [i[1:] for i in maf if i[0] == 'p']
if pLines: classes = map(probabilityClass, zip(*pLines))
else: classes = itertools.repeat(None)
print '<pre>'
for x in range(0, alignmentLength, opts.linesize):
y = x + opts.linesize
seqChunks = [s[x:y] for s in sequences]
classChunk = itertools.islice(classes, x, y)
spans = list(identicalRuns(classChunk))
columnSymbols = map(columnSymbol, zip(*seqChunks))
begs = map(coordinateString, [c+1 for c in coordinates])
begWidth = maxlen(begs)
for i, s in enumerate(seqChunks): coordinates[i] += countOfNonGaps(s)
ends = map(coordinateString, coordinates)
endWidth = maxlen(ends)
for n, b, s, e in zip(names, begs, seqChunks, ends):
print '%-*s' % (nameWidth, n),
print '%*s' % (begWidth, b),
print ''.join(htmlSpans(s, spans)),
print '%*s' % (endWidth, e)
print ' ' * nameWidth, ' ' * begWidth, ''.join(columnSymbols)
print
print '</pre>'
print '</body></html>'
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