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#! /usr/bin/env python
# Copyright 2010 Martin C. Frith
# Read MAF-format alignments: write them in other formats.
import sys, os, fileinput, optparse, itertools, signal
##### General-purpose routines: #####
def flatten(listOfLists): return sum(listOfLists, [])
def valueFromMaf(mafLines, keyword):
for word in mafLines[0]:
if word.startswith(keyword + '='):
return word.split('=')[1]
return ''
def scoreFromMaf(mafLines):
score = valueFromMaf(mafLines, "score")
if not score: raise Exception("encountered an alignment without a score")
return score
##### Routines for converting to AXT format: #####
def axtDataFromMafLine(sLine):
chr = sLine[1]
mafBeg = int(sLine[2])
mafLen = int(sLine[3])
axtBeg = str(mafBeg + 1) # convert from 0-based to 1-based coordinate
axtEnd = str(mafBeg + mafLen)
strand = sLine[4]
return [chr, axtBeg, axtEnd, strand]
axtCounter = itertools.count()
def writeAxt(maf):
count = str(axtCounter.next())
score = scoreFromMaf(maf)
sLines = [i for i in maf if i[0] == "s"]
if not sLines: raise Exception("empty alignment")
sequences = [i[6] for i in sLines]
axtData = map(axtDataFromMafLine, sLines)
dataHead, dataTail = axtData[0], axtData[1:]
if dataHead[3] != "+":
raise Exception("for AXT, the 1st strand in each alignment must be +")
print " ".join([count] + dataHead[:3] + flatten(dataTail) + [score])
for i in sequences: print i
print # print a blank line at the end
##### Routines for converting to tabular format: #####
def gapString(gap1, gap2):
return str(gap1) + ":" + str(gap2)
def symbolSize(symbol, letterSize):
if symbol == "-": return 0
elif symbol == "\\": return 1
elif symbol == "/": return -1
else: return letterSize
def matchAndGapSizes(sequence1, sequence2, letterSize1, letterSize2):
if len(sequence1) != len(sequence2):
raise Exception('aligned sequences have different lengths')
matchSize = 0
gap1 = gap2 = 0
for i, j in zip(sequence1, sequence2):
if '-' in (i, j):
if matchSize != 0:
yield str(matchSize)
matchSize = 0
gap1 += symbolSize(i, letterSize1)
gap2 += symbolSize(j, letterSize2)
else:
if gap1 != 0 or gap2 != 0:
yield gapString(gap1, gap2)
gap1 = gap2 = 0
matchSize += 1 # this is correct for translated alignments too
if matchSize != 0:
yield str(matchSize)
elif gap1 != 0 or gap2 != 0:
yield gapString(gap1, gap2)
def gapSizePerLetter(sLine):
sequence = sLine[6]
if "/" in sequence or "\\" in sequence: return 3
gaps = sequence.count("-")
nonGaps = len(sequence) - gaps
mafLen = int(sLine[3])
if mafLen == nonGaps * 3: return 3
return 1
def writeTab(maf):
score = scoreFromMaf(maf)
expect = valueFromMaf(maf, "expect")
sLines = [i for i in maf if i[0] == "s"]
if len(sLines) != 2: raise Exception("pairwise alignments only, please")
outWords = [i[1:6] for i in sLines]
sequences = [i[6] for i in sLines]
sizes = map(gapSizePerLetter, sLines)
gapInfo = matchAndGapSizes(sequences[0], sequences[1], sizes[0], sizes[1])
gapString = ','.join(gapInfo)
fields = [score] + flatten(outWords) + [gapString]
if expect: fields += [expect]
print "\t".join(fields)
##### Routines for reading MAF format: #####
def mafInput(lines):
maf = []
for line in lines:
if line.startswith("#"):
print line,
elif line.isspace():
if maf: yield maf
maf = []
else:
maf.append(line.split())
if maf: yield maf
def formatName(formatString):
s = formatString.lower()
if "axt".startswith(s): return "axt"
elif "tabular".startswith(s): return "tab"
else: raise Exception("unknown format: " + formatString)
def mafConvert(args):
format = formatName(args[0])
for maf in mafInput(fileinput.input(args[1])):
if format == "axt": writeAxt(maf)
else: writeTab(maf)
if __name__ == "__main__":
signal.signal(signal.SIGPIPE, signal.SIG_DFL) # avoid silly error message
usage = """
%prog axt my-alignments.maf
%prog tab my-alignments.maf"""
op = optparse.OptionParser(usage=usage)
(opts, args) = op.parse_args()
if len(args) != 2: op.error("I need a format-name and a file-name")
try: mafConvert(args)
except KeyboardInterrupt: pass # avoid silly error message
except Exception, e:
prog = os.path.basename(sys.argv[0])
sys.exit(prog + ": error: " + str(e))
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