Mercurial > repos > mzeidler > virana_main
comparison vmap_dnaindex.py @ 0:f63d639b223c draft
Initial Upload
| author | mzeidler |
|---|---|
| date | Wed, 25 Sep 2013 11:41:16 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:f63d639b223c |
|---|---|
| 1 from argparse import ArgumentParser | |
| 2 import os | |
| 3 from vmap import DNAIndex | |
| 4 | |
| 5 if __name__ == "__main__": | |
| 6 | |
| 7 | |
| 8 parser = ArgumentParser() | |
| 9 | |
| 10 a = parser.add_argument | |
| 11 a("-o","--html_file",dest="html_file") | |
| 12 a("-d","--dir",dest="directory") | |
| 13 | |
| 14 (options,args)= parser.parse_known_args() | |
| 15 | |
| 16 args.insert(0,"dummy") | |
| 17 try: | |
| 18 DNAIndex.run(argv=args) | |
| 19 except SystemExit: | |
| 20 f = open(options.html_file,'w') | |
| 21 rval = ["<html><head><title>BWA Index Galaxy Composite Dataset </title></head><body><p/>\n"] | |
| 22 rval.append('<div>This composite dataset is composed of the following files:<p/><ul>') | |
| 23 flist = os.listdir(options.directory) | |
| 24 | |
| 25 for file in flist: | |
| 26 rval.append( '<li><a href="%s">%s</a></li>' % ( file, file) ) | |
| 27 rval.append( '</ul></body></html>' ) | |
| 28 | |
| 29 f.write("\n".join( rval )) | |
| 30 f.close() |