def main(args):
parser = OptionParser('usage: %prog [options]')
optionsAvailable = (
('-i', '--input', 'Sequence_File_ID', 'int',
'Sequence_File_ID from MegaChip.Sequence_File table.'),
('-a', '--alignment', 'Alignment_Protocol_ID', 'int',
('Alignment_Protocol_ID from MegaChip.Alignment_Protocol '
'table.')),
('-t', '--taxonomy', 'Taxonomy_ID', 'int',
'Taxonomy_ID from MegaChipDB.Taxonomy table.'),
('-e','--expect','Alignment_Score_Limit','float',
'Score cutoff for alignment.'),
('-f', '--filter', 'Blast_Filter_Protocol_ID', 'int',
('Blast_Filter_Protocol_ID from MegaChipDB.'
'Blast_Filter_Protocol table. If None no filter will be '
'used.')),
('-l', '--likeTHD', 'templateTHD_ID','int',
'use exsiting THD as template for unspecified values'),
)
ids =[ x[2] for x in optionsAvailable if x[2] != 'templateTHD_ID' ]
for opt in optionsAvailable:
if opt[3] is None:
otype = 'string'
else:
otype = opt[3]
parser.add_option(opt[0], opt[1], dest=opt[2], type=otype,
help=opt[4])
(options, args) = parser.parse_args(args)
defined = lambda x: getattr(options, x) is not None
if options.templateTHD_ID != None:
templateTHD=THD(options.templateTHD_ID)
for opt in ids:
if not defined(opt):
setattr(options,opt,getattr(templateTHD,opt))
if not all(map(defined, ids)):
print >> sys.stderr, ('Usage error: all arguments are required, '
'or derived from template THD')
print >> sys.stderr, parser.format_help()
sys.exit(1)
thdc = THDCreator(options.Sequence_File_ID,
options.Alignment_Protocol_ID,
options.Alignment_Score_Limit,
options.Taxonomy_ID,
options.Blast_Filter_Protocol_ID)
thdc.run()
