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()