Mercurial > repos > davidmurphy > codonlogo
diff inter.py @ 0:c55bdc2fb9fa
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author | davidmurphy |
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date | Thu, 27 Oct 2011 12:09:09 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/inter.py Thu Oct 27 12:09:09 2011 -0400 @@ -0,0 +1,29 @@ +#!/usr/tmp/bin/python2.7 + + +import weblogolib +from corebio.utils.deoptparse import DeOptionParser +import sys + + +#setup +def blackboxcodonl(inputf,outputf): + parser = weblogolib._build_option_parser() + + (opts, args) = parser.parse_args(['--size', 'large', '--composition', 'none', '--fin',inputf,'--fout', outputf]) + + + if args : parser.error("Unparsable arguments: %s " % args) + #best not to change anything in the try except block. + try: + data = weblogolib._build_logodata(opts) + format = weblogolib._build_logoformat(data, opts) + formatter = opts.formatter + formatter(data, format, opts.fout) + except ValueError, err : + print >>sys.stderr, 'Error:', err + sys.exit(2) + except KeyboardInterrupt, err: + sys.exit(0) + +blackboxcodonl('/home/david/examples/cluster17.aln',"outfile.eps")