Mercurial > repos > davidmurphy > codonlogo
comparison inter.py @ 0:c55bdc2fb9fa
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| author | davidmurphy |
|---|---|
| date | Thu, 27 Oct 2011 12:09:09 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:c55bdc2fb9fa |
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| 1 #!/usr/tmp/bin/python2.7 | |
| 2 | |
| 3 | |
| 4 import weblogolib | |
| 5 from corebio.utils.deoptparse import DeOptionParser | |
| 6 import sys | |
| 7 | |
| 8 | |
| 9 #setup | |
| 10 def blackboxcodonl(inputf,outputf): | |
| 11 parser = weblogolib._build_option_parser() | |
| 12 | |
| 13 (opts, args) = parser.parse_args(['--size', 'large', '--composition', 'none', '--fin',inputf,'--fout', outputf]) | |
| 14 | |
| 15 | |
| 16 if args : parser.error("Unparsable arguments: %s " % args) | |
| 17 #best not to change anything in the try except block. | |
| 18 try: | |
| 19 data = weblogolib._build_logodata(opts) | |
| 20 format = weblogolib._build_logoformat(data, opts) | |
| 21 formatter = opts.formatter | |
| 22 formatter(data, format, opts.fout) | |
| 23 except ValueError, err : | |
| 24 print >>sys.stderr, 'Error:', err | |
| 25 sys.exit(2) | |
| 26 except KeyboardInterrupt, err: | |
| 27 sys.exit(0) | |
| 28 | |
| 29 blackboxcodonl('/home/david/examples/cluster17.aln',"outfile.eps") |