parser.add_argument('-f', '--infile', help='input file', type=fpath, default='.') parser.add_argument('-m', '--model', help='model', type=str, default='GTR') parser.add_argument('-n', '--ncat', help='number of categories of gamma-distributed rate variation', type=int, default=4) parser.add_argument('-d', '--datatype', help='datatype = nt (nucleotide), or aa (amino acid)', type=str, default='nt') args = vars(parser.parse_args()) infile = args['infile'] + os.environ['LSB_JOBINDEX'] model = args['model'] datatype = args['datatype'] ncat = args['ncat'] if not os.path.isfile(infile): print 'Input file not found:\n{0}'.format(os.path.abspath(infile)) sys.exit(0) with open(infile) as file: target = os.path.abspath(file.read()) if not os.path.isfile(target): print 'Target file not found:\n{0}'.format(os.path.abspath(target)) sys.exit(0) print target parent_dir = os.path.dirname(target) name = getname(target) record = TCSeqRec(target, file_format='phylip', name=name) record.get_phyml_tree(model=model,ncat=ncat,datatype=datatype) cPickle.dump(record, open('{0}/{1}.pickle'.format(parent_dir, name),'w'))
infile = args['infile'] if index: infile += index if not infile[-1].isdigit(): print '{0} is not correct'.format(infile) sys.exit(1) if not os.path.isfile(infile): print 'Input file not found:\n{0}'.format(os.path.abspath(infile)) sys.exit(0) with open(infile) as file: target = os.path.abspath(file.read()) if not os.path.isfile(target): print 'Target file not found:\n{0}'.format(os.path.abspath(target)) sys.exit(2) print target parent_dir = os.path.dirname(target) name = getname(target) record = TCSeqRec(target, file_format='phylip', name=name) if not os.path.isfile('{0}/{1}.ml.pickle'.format(parent_dir, name)): record.get_phyml_tree(model='GTR', ncat=4, datatype='nt', tmpdir=tmpdir) cPickle.dump( record, open('{0}/{1}.ml.pickle'.format(parent_dir, name), 'w') ) # In future let's just pickle trees; sequences already stored on disk
except: tmpdir = '/tmp' infile = args['infile'] if index: infile += index if not infile[-1].isdigit(): print '{0} is not correct'.format(infile) sys.exit(1) if not os.path.isfile(infile): print 'Input file not found:\n{0}'.format(os.path.abspath(infile)) sys.exit(0) with open(infile) as file: target = os.path.abspath(file.read()) if not os.path.isfile(target): print 'Target file not found:\n{0}'.format(os.path.abspath(target)) sys.exit(2) print target parent_dir = os.path.dirname(target) name = getname(target) record = TCSeqRec(target, file_format='phylip', name=name) if not os.path.isfile('{0}/{1}.ml.pickle'.format(parent_dir, name)): record.get_phyml_tree(model='GTR',ncat=4,datatype='nt', tmpdir=tmpdir) cPickle.dump(record, open('{0}/{1}.ml.pickle'.format(parent_dir, name),'w')) # In future let's just pickle trees; sequences already stored on disk
'--datatype', help='datatype = nt (nucleotide), or aa (amino acid)', type=str, default='nt') args = vars(parser.parse_args()) infile = args['infile'] + os.environ['LSB_JOBINDEX'] model = args['model'] datatype = args['datatype'] ncat = args['ncat'] if not os.path.isfile(infile): print 'Input file not found:\n{0}'.format(os.path.abspath(infile)) sys.exit(0) with open(infile) as file: target = os.path.abspath(file.read()) if not os.path.isfile(target): print 'Target file not found:\n{0}'.format(os.path.abspath(target)) sys.exit(0) print target parent_dir = os.path.dirname(target) name = getname(target) record = TCSeqRec(target, file_format='phylip', name=name) record.get_phyml_tree(model=model, ncat=ncat, datatype=datatype) cPickle.dump(record, open('{0}/{1}.pickle'.format(parent_dir, name), 'w'))