def test_run():
"""Test run for sample vcf file"""
print('neoepitope workflow test')
path = os.path.dirname(os.path.abspath(__file__))
options = config.baseoptions
options['base']['predictors'] = 'netmhcpan' #'mhcflurry'
options['base']['mhc1_alleles'] = 'HLA-A*02:01'
options['base']['path'] = 'neo_test'
#options['base']['mhc2_length'] = 11
#options['base']['verbose'] = True
#options['base']['cpus'] = 4
options['neopredict']['vcf_files'] = os.path.join(path, 'testing',
'input.vcf')
options = config.check_options(options)
#print (options)
W = NeoEpitopeWorkFlow(options)
st = W.setup()
W.run()
def test_run():
"""Test run for a sample file"""
path = os.path.dirname(os.path.abspath(__file__))
options = config.baseoptions
b=options['base']
b['sequence_file'] = os.path.join(path, 'testing','zaire-ebolavirus.faa')
b['mhc1_alleles'] = 'HLA-A*02:01,HLA-A*03:01,HLA-A*23:01'
b['mhc2_alleles'] = 'human_common_mhc2'
b['predictors'] = 'tepitope,mhcflurry'
b['path'] = 'zaire_test'
b['verbose'] = True
b['cutoff_method'] = 'score'
b['cutoffs'] = '5,500'
#b['compression'] = 'gzip'
b['overwrite'] = False
options = config.check_options(options)
W = WorkFlow(options)
st = W.setup()
W.run()
def test_run():
"""Test run for a sample file."""
#installed = ','.join(check_installed())
installed = 'tepitope,mhcflurry,netmhcpan'
path = os.path.dirname(os.path.abspath(__file__))
options = config.baseoptions
b=options['base']
b['sequence_file'] = os.path.join(path, 'testing','zaire-ebolavirus.faa')
b['mhc1_alleles'] = 'HLA-A*02:01,HLA-A*03:01,HLA-A*02:06'
b['mhc2_alleles'] = 'human_common_mhc2'
b['mhc1_length'] = 9
b['predictors'] = installed
b['path'] = 'zaire_test'
b['verbose'] = True
b['cutoff_method'] = 'score'
b['cutoffs'] = '5,500'
b['overwrite'] = True
options = config.check_options(options)
W = WorkFlow(options)
st = W.setup()
W.run()
def main():
"Run the application"
import sys, os
from optparse import OptionParser
parser = OptionParser()
parser.add_option("-c", "--config", dest="config",
help="Configuration file", metavar="FILE")
parser.add_option("-r", "--run", dest="run", action="store_true",
default=False, help="Run the predictions")
parser.add_option("-p", "--presets", dest="presets", action="store_true",
default=False, help="Show preset allele lists")
parser.add_option("-l", "--list-alleles", dest="list_alleles", action="store_true",
default=False, help="List available alleles")
parser.add_option("-t", "--test", dest="test", action="store_true",
default=False, help="Do test predictions")
parser.add_option("-a", "--analysis", dest="analysis",
help="Analysis path", metavar="FILE")
parser.add_option("-n", "--neoepitope", dest="neoepitope", action="store_true",
default=False, help="Neo-epitope pipeline")
parser.add_option("-s", "--server", dest="server", action="store_true",
default=False, help="Run web app")
parser.add_option("-x", "--port", dest="port", default=8000,
help="Port for web app, default 8000")
parser.add_option("-v", "--version", dest="version", action="store_true",
help="Get version")
opts, remainder = parser.parse_args()
if opts.config != None:
cp = config.parse_config(opts.config)
options = config.get_options(cp)
options = config.check_options(options)
else:
conffile = 'default.conf'
if not os.path.exists(conffile):
config.write_config(conffile, defaults=config.baseoptions)
if opts.presets == True:
show_preset_alleles()
elif opts.list_alleles == True:
list_alleles()
elif opts.run == True:
W = WorkFlow(options)
st = W.setup()
if st == True:
W.run()
elif opts.analysis is not None:
W = WorkFlow()
W.analysis(opts.analysis)
elif opts.neoepitope == True:
if opts.test == True:
neo.test_run()
else:
W = neo.NeoEpitopeWorkFlow(options)
st = W.setup()
if st == True:
W.run()
elif opts.server == True:
#from epitopepredict.server import webapp
#webapp.run(port=5000, debug=True)
import epitopepredict.tornado_serve
epitopepredict.tornado_serve.main(opts.port)
elif opts.test == True:
test_run()
elif opts.version == True:
from . import __version__
print ('epitopepredict version %s' %__version__)
else:
print_help()
