Here's my solution to the problem[1]:
[1] http://shootout.alioth.debian.org/benchmark.php?test=revcomp
import sys
import string
basetable = string.maketrans('ACBDGHKMNSRUTWVYacbdghkmnsrutwvy',
'TGVHCDMKNSYAAWBRTGVHCDMKNSYAAWBR')
def revcomp(seqlines, linelength=60, basetable=basetable):
seq = ''.join(seqlines)
complement = seq.translate(basetable)
revcomplement = complement[::-1]
for i in xrange(0, len(revcomplement), linelength):
print revcomplement[i:i+linelength]
def main():
seqlines = []
for line in sys.stdin:
if line.startswith('>') or line.startswith(';'):
if seqlines:
revcomp(seqlines)
sys.stdout.write(line)
seqlines = []
else:
seqlines.append(line.strip())
revcomp(seqlines)
if __name__ == '__main__':
main()
--
Robert Kern
[EMAIL PROTECTED]
"In the fields of hell where the grass grows high
Are the graves of dreams allowed to die."
-- Richard Harter
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