options['o'] = F.absfile(options['o'])
options['useLabel'] = 'useLabel' in options
## options['srcplate'] = [s.strip() for s in U.tolist(options.get('srcplate',[]))]
return options
###########################
# MAIN
###########################
try:
if len(sys.argv) < 2:
_use(_defaultOptions())
options = U.cmdDict(_defaultOptions())
try:
options = cleanOptions(options)
except KeyError, why:
logging.error('missing option: ' + why)
_use(options)
parts = P.PartIndex()
for f in options['src']:
parts.readExcel(f)
targets = P.TargetIndex(srccolumns=[
'vector', 'fragment1', 'fragment2', 'fragment3', 'fragment4'
])
targets.readExcel(options['i'])
'p': self.f_project,
'columns': ['buffer01']
}
self.generictest(options)
def test_distribute_sources(self):
"""distribute.py; distribution with seperate reagent source file"""
import evoware.fileutil as F
options = {
'i': F.testRoot('distribution.xls'),
'src': F.testRoot('distribution_sources.xls'),
'o': 'distribute2.gwl',
'p': self.f_project,
'columns': ['buffer01']
}
self.generictest(options)
if __name__ == '__main__':
## print usage and exit if there is less than 1 command line argument
U.scriptusage(_defaultOptions(), doc=__doc__)
options = U.cmdDict(_defaultOptions()) ## parse commandline options
if 'test' in options:
testing.localTest(debug=('debug' in options))
sys.exit(0)
run(options)
options['src'] = [ F.absfile(f) for f in U.tolist(options['src']) ]
options['o'] = F.absfile(options['o'])
options['useLabel'] = 'useLabel' in options
## options['srcplate'] = [s.strip() for s in U.tolist(options.get('srcplate',[]))]
return options
###########################
# MAIN
###########################
try:
if len(sys.argv) < 2:
_use( _defaultOptions() )
options = U.cmdDict( _defaultOptions() )
try:
options = cleanOptions(options)
except KeyError, why:
logging.error('missing option: ' + why)
_use(options)
parts = P.PartIndex()
for f in options['src']:
parts.readExcel(f)
targets = P.TargetIndex(srccolumns=['template', 'primer1', 'primer2'])
targets.readExcel(options['i'])
cwl = P.CherryWorklist(options['o'], targets, parts, reportErrors=True)