def simulate_from_record(
        self, record, output_dir, name, tmpdir, datatype=None, allow_nonsense=False, split_lengths=None, gene_names=None
    ):

        if not datatype:
            datatype = self.datatype
        if datatype == "protein":
            SeqSim.simulate_from_record_WAG(record, output_dir, name, tmpdir, allow_nonsense, split_lengths, gene_names)
        elif datatype == "dna":
            SeqSim.simulate_from_record_GTR(record, output_dir, name, tmpdir, allow_nonsense, split_lengths, gene_names)
        else:
            print "datatype {0} is not recognised".format(datatype)
    def simulate_from_record(
        self,
        record,
        output_dir,
        name,
        tmpdir,
        datatype=None,
        allow_nonsense=False,
        split_lengths=None,
        gene_names=None,
    ):

        if not datatype:
            datatype = self.datatype
        if datatype == 'protein':
            SeqSim.simulate_from_record_WAG(
                record,
                output_dir,
                name,
                tmpdir,
                allow_nonsense,
                split_lengths,
                gene_names,
            )
        elif datatype == 'dna':
            SeqSim.simulate_from_record_GTR(
                record,
                output_dir,
                name,
                tmpdir,
                allow_nonsense,
                split_lengths,
                gene_names,
            )
        else:
            print 'datatype {0} is not recognised'.format(datatype)
Exemple #3
0
tune = args['tune']
regime = args['regime']
permutation_strength = args['permutations']
permutation_type = args['class_permuter']
master_tree_generator = args['master']
filepath = args['directory']
if 'TEMPORARY_DIRECTORY' in os.environ:
    tmpdir = os.environ['TEMPORARY_DIRECTORY']
else:
    tmpdir = args['temp_directory']
indels = args['indels']
ratevar = args['ratevar']
quiet = args['quiet']
gtp_path = args['geodesic']

sim = SeqSim('base')

sim.hky_model(
    alpha=3.551,
    beta=1,
    Afreq=0.31,
    Cfreq=0.18,
    Gfreq=0.21,
    Tfreq=0.3,
    )

if indels:
    sim.indels()

if ratevar:
    sim.rate_variation()