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#! /usr/bin/env python
# Change the order of sequences in MAF alignments, then make sure the
# top sequence is on the + strand. The MAF spacing might get messed up.
import optparse, fileinput, string, re, signal
signal.signal(signal.SIGPIPE, signal.SIG_DFL) # stop spurious error message
parser = optparse.OptionParser(usage="%prog [options] my-alignments.maf")
parser.add_option("-n", type="int", default=2,
help="move the Nth sequence to the top (default: %default)")
(opts, args) = parser.parse_args()
if opts.n < 1: parser.error("option -n: should be >= 1")
complement = string.maketrans('ACGTNSWRYKMBDHVacgtnswrykmbdhv',
'TGCANSWYRMKVHDBtgcanswyrmkvhdb')
def revcomp(seq):
return seq[::-1].translate(complement)
def flipstrand(strand):
if strand == '-': return '+'
else: return '-'
def flip_s_line(words):
start = int(words[4])
alnsize = int(words[6])
seqsize = int(words[10])
newstart = seqsize - start - alnsize
words[4] = str(newstart)
words[8] = flipstrand(words[8])
words[12] = revcomp(words[12])
def flip_p_line(words):
words[2:-2] = words[-3:1:-1]
def flip_q_line(words):
words[2] = words[2][::-1]
def flip_line(line):
words = re.split(r'(\s+)', line) # keep the spaces
if line.startswith('s'): flip_s_line(words)
elif line.startswith('p'): flip_p_line(words)
elif line.startswith('q'): flip_q_line(words)
return ''.join(words)
def indexOfNthSequence(lines, n):
for i, line in enumerate(lines):
if line.startswith('s'):
if n == 1: return i
n -= 1
parser.error("option -n: should be <= the number of sequences")
def write(lines):
if not lines: return
indexToMove = indexOfNthSequence(lines, opts.n)
lines.insert(1, lines.pop(indexToMove))
if lines[1].split()[4] == '-':
lines = map(flip_line, lines)
print ''.join(lines) # this prints a blank line at the end
lines = []
for line in fileinput.input(args):
if line.startswith('#'):
print line,
elif line.isspace():
write(lines)
lines = []
else:
lines.append(line)
write(lines)
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