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_Phyml.py
# Copyright 2011 by Eric Talevich.  All rights reserved.
# This code is part of the Biopython distribution and governed by its license.
# Please see the LICENSE file that should have been included as part of this
# package.
"""Command-line wrapper for the tree inference program PhyML."""
__docformat__ = "restructuredtext en"

from Bio.Application import _Option, _Switch, AbstractCommandline


00011 class PhymlCommandline(AbstractCommandline):
    """Command-line wrapper for the tree inference program PhyML.

    Homepage: http://www.atgc-montpellier.fr/phyml

    Citations:

    Guindon S, Gascuel O.
    A simple, fast, and accurate algorithm to estimate large phylogenies by maximum
    likelihood.
    Systematic Biology, 2003 Oct;52(5):696-704.
    PubMed PMID: 14530136.

    Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O.
    New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing
    the Performance of PhyML 3.0.
    Systematic Biology, 2010 59(3):307-21.

    """

    def __init__(self, cmd='phyml', **kwargs):
        self.parameters = [
            _Option(['-i', '--input', 'input'],
                """Name of the nucleotide or amino-acid sequence file in PHYLIP
                format.""",
                filename=True,
                is_required=True,
                equate=False,
                ),

            _Option(['-d', '--datatype', 'datatype'],
                """Data type is 'nt' for nucleotide (default) and 'aa' for
                amino-acid sequences.""",
                checker_function=lambda x: x in ('nt', 'aa'),
                equate=False,
                ),

            _Switch(['-q', '--sequential', 'sequential'],
                "Changes interleaved format (default) to sequential format."
                ),

            _Option(['-n', '--multiple', 'multiple'],
                "Number of data sets to analyse (integer).",
                checker_function=(lambda x:
                    isinstance(x, int) or x.isdigit()),
                equate=False,
                ),

            _Switch(['-p', '--pars', 'pars'],
                """Use a minimum parsimony starting tree.
                
                This option is taken into account when the '-u' option is absent
                and when tree topology modifications are to be done.
                """
                ),

            _Option(['-b', '--bootstrap', 'bootstrap'],
                """Number of bootstrap replicates, if value is > 0.

                Otherwise: 

                 0: neither approximate likelihood ratio test nor bootstrap
                    values are computed.
                -1: approximate likelihood ratio test returning aLRT statistics.
                -2: approximate likelihood ratio test returning Chi2-based
                    parametric branch supports.
                -4: SH-like branch supports alone.
                """,
                equate=False,
                ),

            _Option(['-m', '--model', 'model'],
                """Substitution model name.

                Nucleotide-based models:

                HKY85 (default) | JC69 | K80 | F81 | F84 | TN93 | GTR | custom

                For the custom option, a string of six digits identifies the
                model. For instance, 000000 corresponds to F81 (or JC69,
                provided the distribution of nucleotide frequencies is uniform).
                012345 corresponds to GTR. This option can be used for encoding
                any model that is a nested within GTR.

                Amino-acid based models:

                LG (default) | WAG | JTT | MtREV | Dayhoff | DCMut | RtREV |
                CpREV | VT | Blosum62 | MtMam | MtArt | HIVw | HIVb | custom
                """,
                checker_function=(lambda x: x in (
                    # Nucleotide models:
                    'HKY85', 'JC69', 'K80', 'F81', 'F84', 'TN93', 'GTR',
                    # Amino acid models:
                    'LG', 'WAG', 'JTT', 'MtREV', 'Dayhoff', 'DCMut',
                    'RtREV', 'CpREV', 'VT', 'Blosum62', 'MtMam', 'MtArt',
                    'HIVw', 'HIVb')
                    or isinstance(x, int)),
                equate=False,
                ),

            _Option(['-f', 'frequencies'],
                """Character frequencies.

                -f e, m, or "fA fC fG fT"

                e : Empirical frequencies, determined as follows : 

                    - Nucleotide sequences: (Empirical) the equilibrium base
                      frequencies are estimated by counting the occurence of the
                      different bases in the alignment.
                    - Amino-acid sequences: (Empirical) the equilibrium
                      amino-acid frequencies are estimated by counting the
                      occurence of the different amino-acids in the alignment.

                m : ML/model-based frequencies, determined as follows : 

                    - Nucleotide sequences: (ML) the equilibrium base
                      frequencies are estimated using maximum likelihood 
                    - Amino-acid sequences: (Model) the equilibrium amino-acid
                      frequencies are estimated using the frequencies defined by
                      the substitution model.

                "fA fC fG fT" : only valid for nucleotide-based models.
                    fA, fC, fG and fT are floating-point numbers that correspond
                    to the frequencies of A, C, G and T, respectively.
                """,
                filename=True, # ensure ".25 .25 .25 .25" stays quoted
                equate=False,
                ),

            # XXX is the '/' character ok in the long arg name?
            _Option(['-t', '--ts/tv', 'ts_tv_ratio'],
                """Transition/transversion ratio. (DNA sequences only.)

                Can be a fixed positive value (ex:4.0) or e to get the
                maximum-likelihood estimate.
                """,
                equate=False,
                ),

            _Option(['-v', '--pinv', 'prop_invar'],
                """Proportion of invariable sites.

                Can be a fixed value in the range [0,1], or 'e' to get the
                maximum-likelihood estimate.
                """,
                equate=False,
                ),

            _Option(['-c', '--nclasses', 'nclasses'],
                """Number of relative substitution rate categories.

                Default 1. Must be a positive integer.
                """,
                equate=False,
                ),

            _Option(['-a', '--alpha', 'alpha'],
                """Distribution of the gamma distribution shape parameter.

                Can be a fixed positive value, or 'e' to get the
                maximum-likelihood estimate.
                """,
                equate=False,
                ),

            _Option(['-s', '--search', 'search'],
                """Tree topology search operation option.

                Can be one of:

                    NNI : default, fast
                    SPR : a bit slower than NNI
                    BEST : best of NNI and SPR search
                """,
                checker_function=lambda x: x in ('NNI', 'SPR', 'BEST'),
                equate=False,
                ),

            # alt name: user_tree_file
            _Option(['-u', '--inputtree', 'input_tree'],
                "Starting tree filename. The tree must be in Newick format.",
                filename=True,
                equate=False,
                ),

            _Option(['-o', 'optimize'],
                """Specific parameter optimisation.

                tlr : tree topology (t), branch length (l) and
                      rate parameters (r) are optimised.
                tl  : tree topology and branch length are optimised.
                lr  : branch length and rate parameters are optimised. 
                l   : branch length are optimised.
                r   : rate parameters are optimised.
                n   : no parameter is optimised.
                """
                ),

            _Switch(['--rand_start', 'rand_start'],
                """Sets the initial tree to random.

                Only valid if SPR searches are to be performed.
                """,
                ),

            _Option(['--n_rand_starts', 'n_rand_starts'],
                """Number of initial random trees to be used.

                Only valid if SPR searches are to be performed.
                """,
                equate=False,
                ),

            _Option(['--r_seed', 'r_seed'],
                """Seed used to initiate the random number generator.

                Must be an integer.
                """,
                equate=False,
                ),

            _Switch(['--print_site_lnl', 'print_site_lnl'],
                "Print the likelihood for each site in file *_phyml_lk.txt."
                ),

            _Switch(['--print_trace', 'print_trace'],
                """Print each phylogeny explored during the tree search process
                in file *_phyml_trace.txt."""
                ),

            _Option(['--run_id', 'run_id'],
                """Append the given string at the end of each PhyML output file.

                This option may be useful when running simulations involving
                PhyML.
                """,
                checker_function=lambda x: isinstance(x, basestring),
                equate=False,
                ),

            # XXX should this always be set to True?
            _Switch(['--quiet', 'quiet'],
                "No interactive questions (for running in batch mode)."
                ),
                ]
        AbstractCommandline.__init__(self, cmd, **kwargs)


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