/usr/bin/maf-convert is in last-align 921-1.
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The actual contents of the file can be viewed below.
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# Copyright 2010, 2011, 2013, 2014 Martin C. Frith
# Read MAF-format alignments: write them in other formats.
# Seems to work with Python 2.x, x>=6
# By "MAF" we mean "multiple alignment format" described in the UCSC
# Genome FAQ, not e.g. "MIRA assembly format".
from itertools import *
import gzip
import math, optparse, os, signal, sys
def myOpen(fileName):
if fileName == "-":
return sys.stdin
if fileName.endswith(".gz"):
return gzip.open(fileName)
return open(fileName)
def maxlen(s):
return max(map(len, s))
def pairOrDie(sLines, formatName):
if len(sLines) != 2:
e = "for %s, each alignment must have 2 sequences" % formatName
raise Exception(e)
return sLines
def isMatch(alignmentColumn):
# No special treatment of ambiguous bases/residues: same as NCBI BLAST.
first = alignmentColumn[0].upper()
for i in alignmentColumn[1:]:
if i.upper() != first: return False
return True
def gapRunCount(row):
"""Get the number of runs of gap characters."""
return sum(k == "-" for k, v in groupby(row))
def alignmentRowsFromColumns(columns):
return imap(''.join, izip(*columns))
def symbolSize(symbol, letterSize):
if symbol == "\\": return 1
if symbol == "/": return -1
return letterSize
def insertSize(row, letterSize):
"""Get the length of sequence included in the row."""
return (len(row) - row.count("-")) * letterSize - 4 * row.count("/") - 2 * row.count("\\")
def matchAndInsertSizes(alignmentColumns, letterSizes):
"""Get sizes of gapless blocks, and of the inserts between them."""
letterSizeA, letterSizeB = letterSizes
delSize = insSize = subSize = 0
for x, y in alignmentColumns:
if x == "-":
if subSize:
if delSize or insSize: yield str(delSize) + ":" + str(insSize)
yield str(subSize)
delSize = insSize = subSize = 0
insSize += symbolSize(y, letterSizeB)
elif y == "-":
if subSize:
if delSize or insSize: yield str(delSize) + ":" + str(insSize)
yield str(subSize)
delSize = insSize = subSize = 0
delSize += symbolSize(x, letterSizeA)
else:
subSize += 1
if delSize or insSize: yield str(delSize) + ":" + str(insSize)
if subSize: yield str(subSize)
##### Routines for reading MAF format: #####
def updateEvalueParameters(opts, line):
for field in line.split():
try:
k, v = field.split("=")
x = float(v)
if k == "lambda":
opts.bitScoreA = x / math.log(2)
if k == "K":
opts.bitScoreB = math.log(x, 2)
except ValueError:
pass
def scoreAndEvalue(aLine):
score = evalue = None
for i in aLine.split():
if i.startswith("score="):
score = i[6:]
elif i.startswith("E="):
evalue = i[2:]
return score, evalue
def mafInput(opts, lines):
aLine = ""
sLines = []
qLines = []
pLines = []
for line in lines:
if line[0] == "s":
junk, seqName, beg, span, strand, seqLen, row = line.split()
beg = int(beg)
span = int(span)
seqLen = int(seqLen)
if "\\" in row or "/" in row or len(row) - row.count("-") < span:
letterSize = 3
else:
letterSize = 1
fields = seqName, seqLen, strand, letterSize, beg, beg + span, row
sLines.append(fields)
elif line[0] == "a":
aLine = line
elif line[0] == "q":
qLines.append(line)
elif line[0] == "p":
pLines.append(line)
elif line.isspace():
if sLines: yield aLine, sLines, qLines, pLines
aLine = ""
sLines = []
qLines = []
pLines = []
elif line[0] == "#":
updateEvalueParameters(opts, line)
if opts.isKeepComments:
print line,
if sLines: yield aLine, sLines, qLines, pLines
def isJoinable(opts, oldMaf, newMaf):
x = oldMaf[1]
y = newMaf[1]
if x[-1][2] == "-":
x, y = y, x
return all(i[:4] == j[:4] and i[5] <= j[4] and j[4] - i[5] <= opts.join
for i, j in zip(x, y))
def fixOrder(mafs):
sLines = mafs[0][1]
if sLines[-1][2] == "-":
mafs.reverse()
def mafGroupInput(opts, lines):
x = []
for i in mafInput(opts, lines):
if x and not isJoinable(opts, x[-1], i):
fixOrder(x)
yield x
x = []
x.append(i)
if x:
fixOrder(x)
yield x
##### Routines for converting to AXT format: #####
axtCounter = count()
def writeAxt(maf):
aLine, sLines, qLines, pLines = maf
if sLines[0][2] != "+":
raise Exception("for AXT, the 1st strand in each alignment must be +")
# Convert to AXT's 1-based coordinates:
ranges = [(i[0], str(i[4] + 1), str(i[5]), i[2]) for i in sLines]
head, body = ranges[0], ranges[1:]
outWords = [str(next(axtCounter))]
outWords.extend(head[:3])
for i in body:
outWords.extend(i)
score, evalue = scoreAndEvalue(aLine)
if score:
outWords.append(score)
print " ".join(outWords)
for i in sLines:
print i[6]
print # print a blank line at the end
def mafConvertToAxt(opts, lines):
for maf in mafInput(opts, lines):
writeAxt(maf)
##### Routines for converting to tabular format: #####
def writeTab(maf):
aLine, sLines, qLines, pLines = maf
score = "0"
endWords = []
for i in aLine.split():
if i.startswith("score="):
score = i[6:]
elif len(i) > 1:
endWords.append(i)
outWords = [score]
for seqName, seqLen, strand, letterSize, beg, end, row in sLines:
x = seqName, str(beg), str(end - beg), strand, str(seqLen)
outWords.extend(x)
letterSizes = [i[3] for i in sLines]
rows = [i[6] for i in sLines]
alignmentColumns = izip(*rows)
gapWord = ",".join(matchAndInsertSizes(alignmentColumns, letterSizes))
outWords.append(gapWord)
print "\t".join(outWords + endWords)
def mafConvertToTab(opts, lines):
for maf in mafInput(opts, lines):
writeTab(maf)
##### Routines for converting to chain format: #####
def writeChain(maf):
aLine, sLines, qLines, pLines = maf
score = "0"
for i in aLine.split():
if i.startswith("score="):
score = i[6:]
outWords = ["chain", score]
for seqName, seqLen, strand, letterSize, beg, end, row in sLines:
x = seqName, str(seqLen), strand, str(beg), str(end)
outWords.extend(x)
outWords.append(str(next(axtCounter) + 1))
print " ".join(outWords)
letterSizes = [i[3] for i in sLines]
rows = [i[6] for i in sLines]
alignmentColumns = izip(*rows)
size = "0"
for i in matchAndInsertSizes(alignmentColumns, letterSizes):
if ":" in i:
print size + "\t" + i.replace(":", "\t")
size = "0"
else:
size = i
print size
def mafConvertToChain(opts, lines):
for maf in mafInput(opts, lines):
writeChain(maf)
##### Routines for converting to PSL format: #####
def pslBlocks(opts, mafs, outCounts):
"""Get sizes and start coordinates of gapless blocks in an alignment."""
# repMatches is always zero
# for proteins, nCount is always zero, because that's what BLATv34 does
normalBases = "ACGTU"
matches = mismatches = repMatches = nCount = 0
for maf in mafs:
sLines = maf[1]
fieldsA, fieldsB = pairOrDie(sLines, "PSL")
letterSizeA, begA, endA, rowA = fieldsA[3:7]
letterSizeB, begB, endB, rowB = fieldsB[3:7]
size = 0
for x, y in izip(rowA.upper(), rowB.upper()):
if x == "-":
if size:
yield size, begA, begB
begA += size * letterSizeA
begB += size * letterSizeB
size = 0
begB += symbolSize(y, letterSizeB)
elif y == "-":
if size:
yield size, begA, begB
begA += size * letterSizeA
begB += size * letterSizeB
size = 0
begA += symbolSize(x, letterSizeA)
else:
size += 1
if x in normalBases and y in normalBases or opts.protein:
if x == y:
matches += 1
else:
mismatches += 1
else:
nCount += 1
if size:
yield size, begA, begB
outCounts[0:4] = matches, mismatches, repMatches, nCount
def pslNumInserts(blocks, letterSizeA, letterSizeB):
numInsertA = numInsertB = 0
for i, x in enumerate(blocks):
size, begA, begB = x
if i:
if begA > endA:
numInsertA += 1
if begB > endB:
numInsertB += 1
endA = begA + size * letterSizeA
endB = begB + size * letterSizeB
return numInsertA, numInsertB
def pslCommaString(things):
# UCSC software seems to prefer a trailing comma
return ",".join(map(str, things)) + ","
def pslEnds(seqLen, strand, beg, end):
if strand == "-":
return seqLen - end, seqLen - beg
return beg, end
def writePsl(opts, mafs):
matchCounts = [0] * 4
blocks = list(pslBlocks(opts, mafs, matchCounts))
matches, mismatches, repMatches, nCount = matchCounts
numGaplessColumns = sum(matchCounts)
if not blocks:
return
fieldsA, fieldsB = mafs[0][1]
headSize, headBegA, headBegB = blocks[0]
tailSize, tailBegA, tailBegB = blocks[-1]
seqNameA, seqLenA, strandA, letterSizeA = fieldsA[0:4]
begA, endA = pslEnds(seqLenA, strandA, headBegA, tailBegA + tailSize)
baseInsertA = endA - begA - numGaplessColumns * letterSizeA
seqNameB, seqLenB, strandB, letterSizeB = fieldsB[0:4]
begB, endB = pslEnds(seqLenB, strandB, headBegB, tailBegB + tailSize)
baseInsertB = endB - begB - numGaplessColumns * letterSizeB
numInsertA, numInsertB = pslNumInserts(blocks, letterSizeA, letterSizeB)
strand = strandB
if letterSizeA > 1 or letterSizeB > 1:
strand += strandA
elif strandA != "+":
raise Exception("for non-translated PSL, the 1st strand in each alignment must be +")
blockCount = len(blocks)
blockSizes, blockStartsA, blockStartsB = map(pslCommaString, zip(*blocks))
outWords = (matches, mismatches, repMatches, nCount,
numInsertB, baseInsertB, numInsertA, baseInsertA, strand,
seqNameB, seqLenB, begB, endB, seqNameA, seqLenA, begA, endA,
blockCount, blockSizes, blockStartsB, blockStartsA)
print "\t".join(map(str, outWords))
def mafConvertToPsl(opts, lines):
if opts.join:
for i in mafGroupInput(opts, lines):
writePsl(opts, i)
else:
for i in mafInput(opts, lines):
writePsl(opts, [i])
##### Routines for converting to SAM format: #####
def readGroupId(readGroupItems):
for i in readGroupItems:
if i.startswith("ID:"):
return i[3:]
raise Exception("readgroup must include ID")
def readSequenceLengths(fileNames):
"""Read name & length of topmost sequence in each maf block."""
for i in fileNames:
f = myOpen(i)
fields = None
for line in f:
if fields:
if line.isspace():
fields = None
else:
if line[0] == "s":
fields = line.split()
yield fields[1], fields[5]
f.close()
def naturalSortKey(s):
"""Return a key that sorts strings in "natural" order."""
return [(str, int)[k]("".join(v)) for k, v in groupby(s, str.isdigit)]
def karyotypicSortKey(s):
"""Attempt to sort chromosomes in GATK's ridiculous order."""
if s == "chrM": return []
if s == "MT": return ["~"]
return naturalSortKey(s)
def copyDictFile(lines):
for line in lines:
if line.startswith("@SQ"):
sys.stdout.write(line)
elif not line[0] == "@":
break
def writeSamHeader(opts, fileNames):
print "@HD\tVN:1.3\tSO:unsorted"
if opts.dictionary:
sequenceLengths = dict(readSequenceLengths(fileNames))
for k in sorted(sequenceLengths, key=karyotypicSortKey):
print "@SQ\tSN:%s\tLN:%s" % (k, sequenceLengths[k])
if opts.dictfile:
f = myOpen(opts.dictfile)
copyDictFile(f)
f.close()
if opts.readgroup:
print "@RG\t" + "\t".join(opts.readgroup.split())
mapqMissing = "255"
mapqMaximum = "254"
mapqMaximumNum = float(mapqMaximum)
def mapqFromProb(probString):
try: p = float(probString)
except ValueError: raise Exception("bad probability: " + probString)
if p < 0 or p > 1: raise Exception("bad probability: " + probString)
if p == 0: return mapqMaximum
phred = -10 * math.log(p, 10)
if phred >= mapqMaximumNum: return mapqMaximum
return str(int(round(phred)))
def cigarParts(beg, alignmentColumns, end):
if beg: yield str(beg) + "H"
# (doesn't handle translated alignments)
# uses "read-ahead" technique, aiming to be as fast as possible:
isActive = True
for x, y in alignmentColumns: break
else: isActive = False
while isActive:
size = 1
if x == y: # xxx assumes no gap-gap columns, ignores ambiguous bases
for x, y in alignmentColumns:
if x != y: break
size += 1
else: isActive = False
yield str(size) + "="
elif x == "-":
for x, y in alignmentColumns:
if x != "-": break
size += 1
else: isActive = False
yield str(size) + "I"
elif y == "-":
for x, y in alignmentColumns:
if y != "-": break
size += 1
else: isActive = False
yield str(size) + "D"
else:
for x, y in alignmentColumns:
if x == y or x == "-" or y == "-": break
size += 1
else: isActive = False
yield str(size) + "X"
if end: yield str(end) + "H"
def writeSam(readGroup, maf):
aLine, sLines, qLines, pLines = maf
fieldsA, fieldsB = pairOrDie(sLines, "SAM")
seqNameA, seqLenA, strandA, letterSizeA, begA, endA, rowA = fieldsA
seqNameB, seqLenB, strandB, letterSizeB, begB, endB, rowB = fieldsB
if letterSizeA > 1 or letterSizeB > 1:
raise Exception("this looks like translated DNA - can't convert to SAM format")
if strandA != "+":
raise Exception("for SAM, the 1st strand in each alignment must be +")
score = None
evalue = None
mapq = mapqMissing
for i in aLine.split():
if i.startswith("score="):
v = i[6:]
if v.isdigit(): score = "AS:i:" + v # it must be an integer
elif i.startswith("E="):
evalue = "EV:Z:" + i[2:]
elif i.startswith("mismap="):
mapq = mapqFromProb(i[7:])
pos = str(begA + 1) # convert to 1-based coordinate
alignmentColumns = zip(rowA.upper(), rowB.upper())
revBegB = seqLenB - endB
cigar = "".join(cigarParts(begB, iter(alignmentColumns), revBegB))
seq = rowB.translate(None, "-")
qual = "*"
if qLines:
qFields = qLines[-1].split()
if qFields[1] == seqNameB:
qual = ''.join(j for i, j in izip(rowB, qFields[2]) if i != "-")
# It's hard to get all the pair info, so this is very
# incomplete, but hopefully good enough.
# I'm not sure whether to add 2 and/or 8 to flag.
if seqNameB.endswith("/1"):
seqNameB = seqNameB[:-2]
if strandB == "+": flag = "99" # 1 + 2 + 32 + 64
else: flag = "83" # 1 + 2 + 16 + 64
elif seqNameB.endswith("/2"):
seqNameB = seqNameB[:-2]
if strandB == "+": flag = "163" # 1 + 2 + 32 + 128
else: flag = "147" # 1 + 2 + 16 + 128
else:
if strandB == "+": flag = "0"
else: flag = "16"
editDistance = sum(x != y for x, y in alignmentColumns)
# no special treatment of ambiguous bases: might be a minor bug
editDistance = "NM:i:" + str(editDistance)
out = [seqNameB, flag, seqNameA, pos, mapq, cigar, "*\t0\t0", seq, qual]
out.append(editDistance)
if score: out.append(score)
if evalue: out.append(evalue)
if readGroup: out.append(readGroup)
print "\t".join(out)
def mafConvertToSam(opts, lines):
readGroup = ""
if opts.readgroup:
readGroup = "RG:Z:" + readGroupId(opts.readgroup.split())
for maf in mafInput(opts, lines):
writeSam(readGroup, maf)
##### Routines for converting to BLAST-like format: #####
def pairwiseMatchSymbol(alignmentColumn):
if isMatch(alignmentColumn):
return "|"
else:
return " "
def strandText(strand):
if strand == "+":
return "Plus"
else:
return "Minus"
def blastBegCoordinate(zeroBasedCoordinate, strand, seqLen):
if strand == "+":
return str(zeroBasedCoordinate + 1)
else:
return str(seqLen - zeroBasedCoordinate)
def blastEndCoordinate(zeroBasedCoordinate, strand, seqLen):
if strand == "+":
return str(zeroBasedCoordinate)
else:
return str(seqLen - zeroBasedCoordinate + 1)
def nextCoordinate(coordinate, row, letterSize):
return coordinate + insertSize(row, letterSize)
def chunker(things, chunkSize):
for i in range(0, len(things), chunkSize):
yield things[i:i+chunkSize]
def blastChunker(sLines, lineSize, alignmentColumns):
seqLens = [i[1] for i in sLines]
strands = [i[2] for i in sLines]
letterSizes = [i[3] for i in sLines]
coords = [i[4] for i in sLines]
for chunkCols in chunker(alignmentColumns, lineSize):
chunkRows = list(alignmentRowsFromColumns(chunkCols))
begs = map(blastBegCoordinate, coords, strands, seqLens)
coords = map(nextCoordinate, coords, chunkRows, letterSizes)
ends = map(blastEndCoordinate, coords, strands, seqLens)
yield chunkCols, chunkRows, begs, ends
def writeBlast(opts, maf, oldQueryName):
aLine, sLines, qLines, pLines = maf
fieldsA, fieldsB = pairOrDie(sLines, "Blast")
seqNameA, seqLenA, strandA, letterSizeA, begA, endA, rowA = fieldsA
seqNameB, seqLenB, strandB, letterSizeB, begB, endB, rowB = fieldsB
if seqNameB != oldQueryName:
print "Query= " + seqNameB
print " (%s letters)" % seqLenB
print
print ">" + seqNameA
print " Length = %s" % seqLenA
print
score, evalue = scoreAndEvalue(aLine)
if score and opts.bitScoreA is not None and opts.bitScoreB is not None:
bitScore = opts.bitScoreA * float(score) - opts.bitScoreB
scoreLine = " Score = %.3g bits (%s)" % (bitScore, score)
else:
scoreLine = " Score = %s" % score
if evalue:
scoreLine += ", Expect = %s" % evalue
print scoreLine
alignmentColumns = zip(rowA, rowB)
alnSize = len(alignmentColumns)
matches = sum(x.upper() == y.upper() for x, y in alignmentColumns)
matchPercent = 100 * matches // alnSize # round down, like BLAST
identLine = " Identities = %s/%s (%s%%)" % (matches, alnSize, matchPercent)
gaps = rowA.count("-") + rowB.count("-")
if gaps:
gapPercent = 100 * gaps // alnSize # round down, like BLAST
identLine += ", Gaps = %s/%s (%s%%)" % (gaps, alnSize, gapPercent)
print identLine
print " Strand = %s / %s" % (strandText(strandB), strandText(strandA))
print
for chunk in blastChunker(sLines, opts.linesize, alignmentColumns):
cols, rows, begs, ends = chunk
begWidth = maxlen(begs)
matchSymbols = ''.join(map(pairwiseMatchSymbol, cols))
print "Query: %-*s %s %s" % (begWidth, begs[1], rows[1], ends[1])
print " %-*s %s" % (begWidth, " ", matchSymbols)
print "Sbjct: %-*s %s %s" % (begWidth, begs[0], rows[0], ends[0])
print
def mafConvertToBlast(opts, lines):
oldQueryName = ""
for maf in mafInput(opts, lines):
writeBlast(opts, maf, oldQueryName)
sLines = maf[1]
oldQueryName = sLines[1][0]
def blastDataFromMafFields(fields):
seqName, seqLen, strand, letterSize, beg, end, row = fields
if strand == "+":
beg += 1
else:
beg = seqLen - beg
end = seqLen - end + 1
return seqName, str(beg), str(end), row.upper()
def writeBlastTab(opts, maf):
aLine, sLines, qLines, pLines = maf
fieldsA, fieldsB = pairOrDie(sLines, "BlastTab")
seqNameA, begA, endA, rowA = blastDataFromMafFields(fieldsA)
seqNameB, begB, endB, rowB = blastDataFromMafFields(fieldsB)
alignmentColumns = zip(rowA, rowB)
alnSize = len(alignmentColumns)
matches = sum(x == y for x, y in alignmentColumns)
matchPercent = "%.2f" % (100.0 * matches / alnSize)
mismatches = alnSize - matches - rowA.count("-") - rowB.count("-")
gapOpens = gapRunCount(rowA) + gapRunCount(rowB)
out = [seqNameB, seqNameA, matchPercent, str(alnSize), str(mismatches),
str(gapOpens), begB, endB, begA, endA]
score, evalue = scoreAndEvalue(aLine)
if evalue:
out.append(evalue)
if score and opts.bitScoreA is not None and opts.bitScoreB is not None:
bitScore = opts.bitScoreA * float(score) - opts.bitScoreB
out.append("%.3g" % bitScore)
print "\t".join(out)
def mafConvertToBlastTab(opts, lines):
for maf in mafInput(opts, lines):
writeBlastTab(opts, maf)
##### Routines for converting to HTML format: #####
def writeHtmlHeader():
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">
/* Try to force monospace, working around browser insanity: */
pre {font-family: "Courier New", monospace, serif; font-size: 0.8125em}
.a {background-color: #3333FF}
.b {background-color: #9933FF}
.c {background-color: #FF66CC}
.d {background-color: #FF3333}
.e {background-color: #FF9933}
.f {background-color: #FFFF00}
.key {display:inline; margin-right:2em}
</style>
</head><body>
<div style="line-height:1">
<pre class="key"><span class="a"> </span> prob > 0.999</pre>
<pre class="key"><span class="b"> </span> prob > 0.99 </pre>
<pre class="key"><span class="c"> </span> prob > 0.95 </pre>
<pre class="key"><span class="d"> </span> prob > 0.9 </pre>
<pre class="key"><span class="e"> </span> prob > 0.5 </pre>
<pre class="key"><span class="f"> </span> prob ≤ 0.5 </pre>
</div>
'''
def probabilityClass(probabilityColumn):
p = ord(min(probabilityColumn)) - 33
if p >= 30: return 'a'
elif p >= 20: return 'b'
elif p >= 13: return 'c'
elif p >= 10: return 'd'
elif p >= 3: return 'e'
else: return 'f'
def identicalRuns(s):
"""Yield (item, start, end) for each run of identical items in s."""
beg = 0
for k, v in groupby(s):
end = beg + len(list(v))
yield k, beg, end
beg = end
def htmlSpan(text, classRun):
key, beg, end = classRun
textbit = text[beg:end]
if key: return '<span class="%s">%s</span>' % (key, textbit)
else: return textbit
def multipleMatchSymbol(alignmentColumn):
if isMatch(alignmentColumn): return "*"
else: return " "
def writeHtml(opts, maf):
aLine, sLines, qLines, pLines = maf
scoreLine = "Alignment"
score, evalue = scoreAndEvalue(aLine)
if score:
scoreLine += " score=" + score
if evalue:
scoreLine += ", expect=" + evalue
print "<h3>%s:</h3>" % scoreLine
if pLines:
probRows = [i.split()[1] for i in pLines]
probCols = izip(*probRows)
classes = imap(probabilityClass, probCols)
else:
classes = repeat(None)
seqNames = [i[0] for i in sLines]
nameWidth = maxlen(seqNames)
rows = [i[6] for i in sLines]
alignmentColumns = zip(*rows)
print '<pre>'
for chunk in blastChunker(sLines, opts.linesize, alignmentColumns):
cols, rows, begs, ends = chunk
begWidth = maxlen(begs)
endWidth = maxlen(ends)
matchSymbols = ''.join(map(multipleMatchSymbol, cols))
classChunk = islice(classes, opts.linesize)
classRuns = list(identicalRuns(classChunk))
for n, b, r, e in zip(seqNames, begs, rows, ends):
spans = [htmlSpan(r, i) for i in classRuns]
spans = ''.join(spans)
formatParams = nameWidth, n, begWidth, b, spans, endWidth, e
print '%-*s %*s %s %*s' % formatParams
print ' ' * nameWidth, ' ' * begWidth, matchSymbols
print
print '</pre>'
def mafConvertToHtml(opts, lines):
for maf in mafInput(opts, lines):
writeHtml(opts, maf)
##### Main program: #####
def isFormat(myString, myFormat):
return myFormat.startswith(myString)
def mafConvertOneFile(opts, formatName, lines):
if isFormat(formatName, "axt"):
mafConvertToAxt(opts, lines)
elif isFormat(formatName, "blast"):
mafConvertToBlast(opts, lines)
elif isFormat(formatName, "blasttab"):
mafConvertToBlastTab(opts, lines)
elif isFormat(formatName, "chain"):
mafConvertToChain(opts, lines)
elif isFormat(formatName, "html"):
mafConvertToHtml(opts, lines)
elif isFormat(formatName, "psl"):
mafConvertToPsl(opts, lines)
elif isFormat(formatName, "sam"):
mafConvertToSam(opts, lines)
elif isFormat(formatName, "tabular"):
mafConvertToTab(opts, lines)
else:
raise Exception("unknown format: " + formatName)
def mafConvert(opts, args):
formatName = args[0].lower()
fileNames = args[1:]
opts.isKeepComments = False
opts.bitScoreA = None
opts.bitScoreB = None
if not opts.noheader:
if isFormat(formatName, "html"):
writeHtmlHeader()
if isFormat(formatName, "sam"):
writeSamHeader(opts, fileNames)
if isFormat(formatName, "tabular"):
opts.isKeepComments = True
if not fileNames:
fileNames = ["-"]
for i in fileNames:
f = myOpen(i)
mafConvertOneFile(opts, formatName, f)
f.close()
if not opts.noheader:
if isFormat(formatName, "html"):
print "</body></html>"
if __name__ == "__main__":
signal.signal(signal.SIGPIPE, signal.SIG_DFL) # avoid silly error message
usage = """
%prog --help
%prog axt mafFile(s)
%prog blast mafFile(s)
%prog blasttab mafFile(s)
%prog chain mafFile(s)
%prog html mafFile(s)
%prog psl mafFile(s)
%prog sam mafFile(s)
%prog tab mafFile(s)"""
description = "Read MAF-format alignments & write them in another format."
op = optparse.OptionParser(usage=usage, description=description)
op.add_option("-p", "--protein", action="store_true",
help="assume protein alignments, for psl match counts")
op.add_option("-j", "--join", type="float", metavar="N",
help="join co-linear alignments separated by <= N letters")
op.add_option("-n", "--noheader", action="store_true",
help="omit any header lines from the output")
op.add_option("-d", "--dictionary", action="store_true",
help="include dictionary of sequence lengths in sam format")
op.add_option("-f", "--dictfile",
help="get sequence dictionary from DICTFILE")
op.add_option("-r", "--readgroup",
help="read group info for sam format")
op.add_option("-l", "--linesize", type="int", default=60, #metavar="CHARS",
help="line length for blast and html formats (default: %default)")
opts, args = op.parse_args()
if opts.linesize <= 0: op.error("option -l: should be >= 1")
if opts.dictionary and opts.dictfile: op.error("can't use both -d and -f")
if len(args) < 1: op.error("I need a format-name and some MAF alignments")
if opts.dictionary and (len(args) == 1 or "-" in args[1:]):
op.error("need file (not pipe) with option -d")
try: mafConvert(opts, args)
except Exception, e:
prog = os.path.basename(sys.argv[0])
sys.exit(prog + ": error: " + str(e))
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