python-cogent 1.5.3-2 / usr / share / pyshared / cogent / app / raxml.py

#!/usr/bin/env python
"""Application controller for RAxML (v7.0.3).

WARNING: Because of the use of the -x option, this version is no longer
compatible with RAxML version VI.
"""
from cogent.app.parameters import FlagParameter, ValuedParameter, FilePath
from cogent.app.util import CommandLineApplication, ResultPath, get_tmp_filename
from cogent.core.tree import PhyloNode
from cogent.core.alignment import Alignment
from cogent.core.moltype import DNA, RNA, PROTEIN
from cogent.util.warning import deprecated
from random import choice, randint
from os import walk
from os.path import isabs
from cogent.parse.tree import DndParser

__author__ = "Micah Hamady"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Micah Hamady", "Catherine Lozupone", "Rob Knight", \
               "Daniel McDonald", "Jai Ram Rideout"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Micah Hamady"
__email__ = "hamady@colorado.edu"
__status__ = "Prototype"

class Raxml(CommandLineApplication):
    """RAxML application controller"""

    deprecated('class',
               'cogent.app.raxml.Raxml',
               'cogent.app.raxml_v730.Raxml',
               '1.6')

    _options ={

        # Specify a column weight file name to assign individual wieghts to 
        # each column of the alignment. Those weights must be integers 
        # separated by any number and type of whitespaces whithin a separate 
        # file, see file "example_weights" for an example.
        '-a':ValuedParameter('-',Name='a',Delimiter=' '),

        #  Specify an integer number (random seed) for bootstrapping
        '-b':ValuedParameter('-',Name='b',Delimiter=' '),


        # Specify number of distinct rate catgories for raxml when 
        # ModelOfEvolution is set to GTRCAT or HKY85CAT.
        # Individual per-site rates are categorized into numberOfCategories 
        # rate categories to accelerate computations. (Default = 50)
        '-c':ValuedParameter('-',Name='c',Delimiter=' ', Value=50),

        # This option allows you to start the RAxML search with a complete 
        # random starting tree instead of the default Maximum Parsimony 
        # Starting tree. On smaller datasets (around 100-200 taxa) it has 
        # been observed that this might sometimes yield topologies of distinct 
        # local likelihood maxima which better correspond to empirical 
        # expectations. 
        '-d':FlagParameter('-',Name='d'),

        # This allows you to specify up to which likelihood difference.
        # Default is 0.1 log likelihood units, author recommends 1 or 2 to
        # rapidly evaluate different trees.
        
        '-e':ValuedParameter('-',Name='e',Delimiter=' ', Value=0.1),
        

        # select search algorithm: 
        #   d for normal hill-climbing search (Default)
        #     when -f option is omitted this algorithm will be used
        #   o old (slower) algorithm from v. 2.1.3
        #   c (check) just tests whether it can read the alignment
        #   e (evaluate) to optimize model+branch lengths for given input tree
        #   b (bipartition) draws bipartitions
        #   s (split) splits into individual genes, provided with model file
        '-f':ValuedParameter('-',Name='f',Delimiter=' ', Value="d"),

        # select grouping file name: allows incomplete multifurcating constraint
        # tree in newick format -- resolves multifurcations randomly, adds
        # other taxa using parsimony insertion
        '-g':ValuedParameter('-', Name='g',Delimiter=' '),

        # prints help and exits

        '-h':FlagParameter('-', Name='h'),

        # allows initial rearrangement to be constrained, e.g. 10 means
        # insertion will not be more than 10 nodes away from original.
        # default is to pick a "good" setting.

        '-i':ValuedParameter('-', Name='i', Delimiter=' '),

        # writes checkpoints (off by default)

        '-j':FlagParameter('-', Name='j'),

        #specifies that RAxML will optimize model parameters (for GTRMIX and
        # GTRGAMMA) as well as calculating likelihoods for bootstrapped trees.

        '-k':FlagParameter('-', Name='k'),

        # Model of Nucleotide Substitution:
        # -m GTRGAMMA: GTR + Optimization of substitution rates + Gamma
        # -m GTRCAT: GTR + Optimization of substitution rates +  Optimization 
        #    of site-specific evolutionary rates which are categorized into 
        #    numberOfCategories distinct rate categories for greater 
        #    computational efficiency
        # -m GTRMIX: Searches for GTRCAT, then switches to GTRGAMMA
        
        # Amino Acid Models
        # matrixName (see below): DAYHOFF, DCMUT, JTT, MTREV, WAG, RTREV, 
        # CPREV, VT, BLOSUM62, MTMAM, GTR.
        # F means use empirical nucleotide frequencies (append to string)
        # -m PROTCATmatrixName[F]: uses site-specific rate categories
        # -m PROTGAMMAmatrixName[F]: uses Gamma
        # -m PROTMIXmatrixName[F]: switches between gamma and cat models
        # e.g. -m PROTCATBLOSUM62F would use protcat with BLOSUM62 and
        # empirical frequencies

        '-m':ValuedParameter('-',Name='m',Delimiter=' '),

        # Specifies the name of the output file.
        '-n':ValuedParameter('-',Name='n',Delimiter=' '),

        # Specifies the name of the outgroup (or outgroups: comma-delimited,
        # no spaces, should be monophyletic).
        '-o':ValuedParameter('-',Name='o',Delimiter=' '),

        # Specified MultipleModel file name, in format:
        #    gene1 = 1-500
        #    gene2 = 501-1000
        #    (note: ranges can also be discontiguous, e.g. 1-100, 200-300,
        #     or can specify codon ranges as e.g. 1-100/3, 2-100/3, 3-100/3))
        '-q':ValuedParameter('-', Name='q', Delimiter=' '),

        # Name of the working directory where RAxML-V will write its output 
        # files.
        '-w':ValuedParameter('-',Name='w',Delimiter=' '),

        # Constraint file name: allows a bifurcating Newick tree to be passed
        # in as a constraint file, other taxa will be added by parsimony.
        '-r':ValuedParameter('-',Name='r',Delimiter=' '),
       
        # Specify a random number seed for the parsimony inferences. This 
        # allows you to reproduce your results and will help me debug the 
        # program. This option HAS NO EFFECT in the parallel MPI version
        '-p':ValuedParameter('-',Name='p',Delimiter=' '),
        
        # specify the name of the alignment data file, in relaxed PHYLIP
        # format.
        '-s':ValuedParameter('-',Name='s',Delimiter=' '),

        # Specify a user starting tree file name in Newick format
        '-t':ValuedParameter('-',Name='t',Delimiter=' '),

        # Print the version
        '-v':FlagParameter('-',Name='v'),

        # Compute only randomized starting parsimony tree with RAxML, do not
        # optimize an ML analysis of the tree
        '-y':FlagParameter('-', Name='y'),

        # Multiple tree file, for use with -f b (to draw bipartitions onto the
        # common tree specified with -t)
        '-z':ValuedParameter('-', Name='z', Delimiter=' '),

        # Specifies number of runs on distinct starting trees.
        '-#':ValuedParameter('-', Name='#', Delimiter=' '),

        #Specify an integer number (random seed) to turn on rapid bootstrapping
        '-x':ValuedParameter('-', Name='x', Delimiter=' ')
    }

    _parameters = {}
    _parameters.update(_options)
    _command = "raxmlHPC"
    _out_format = "RAxML_%s.%s"

    def _format_output(self, outfile_name, out_type):
        """ Prepend proper output prefix to output filename """

        outfile_name = self._absolute(outfile_name)
        outparts = outfile_name.split("/") 
        outparts[-1] = self._out_format % (out_type, outparts[-1] )

        return '/'.join(outparts)
 

    def _input_as_seqs(self,data):
        lines = []
        for i,s in enumerate(data):
            #will number the sequences 1,2,3,etc.
            lines.append(''.join(['>',str(i+1)]))
            lines.append(s)
        return self._input_as_lines(lines)

    def _input_as_lines(self,data):
        if data:
            self.Parameters['-s']\
                .on(super(Raxml,self)._input_as_lines(data))
        return ''

    def _input_as_string(self,data):
        """Makes data the value of a specific parameter
     
        This method returns the empty string. The parameter will be printed
        automatically once set.
        """
        if data:
            self.Parameters['-in'].on(str(data))
        return ''

    def _input_as_multiline_string(self, data):
        if data:
            self.Parameters['-s']\
                .on(super(Raxml,self)._input_as_multiline_string(data))
        return ''
   
    def _absolute(self,path):
        path = FilePath(path)
        if isabs(path):
            return path
        elif self.Parameters['-w'].isOn():
            return self.Parameters['-w'].Value + path
        else:
            return self.WorkingDir + path

    def _log_out_filename(self):
        if self.Parameters['-n'].isOn():
            return self._format_output(str(self.Parameters['-n'].Value), "log")
        else:
            raise ValueError, "No output file specified." 

    def _info_out_filename(self):
        if self.Parameters['-n'].isOn():
            return self._format_output(str(self.Parameters['-n'].Value), "info")
        else:
            raise ValueError, "No output file specified." 

    def _parsimony_tree_out_filename(self):
        if self.Parameters['-n'].isOn():
            return self._format_output(str(self.Parameters['-n'].Value), "parsimonyTree")
        else:
            raise ValueError, "No output file specified." 

    def _result_tree_out_filename(self):
        if self.Parameters['-n'].isOn():
            return self._format_output(str(self.Parameters['-n'].Value), "result")
        else:
            raise ValueError, "No output file specified." 

    def _result_bootstrap_out_filename(self):
        if self.Parameters['-n'].isOn():
            return self._format_output(str(self.Parameters['-n'].Value), \
                                       "bootstrap")
        else:
            raise ValueError, "No output file specified"

    def _checkpoint_out_filenames(self):
        """
        RAxML generates a crapload of checkpoint files so need to
        walk directory to collect names of all of them.
        """
        out_filenames = []
        if self.Parameters['-n'].isOn():
            out_name = str(self.Parameters['-n'].Value)
            walk_root = self.WorkingDir
            if self.Parameters['-w'].isOn(): 
                walk_root = str(self.Parameters['-w'].Value)
            for tup in walk(walk_root):
                dpath, dnames, dfiles = tup
                if dpath == walk_root:
                    for gen_file in dfiles:
                        if out_name in gen_file and "checkpoint" in gen_file:
                            out_filenames.append(walk_root + gen_file)
                    break

        else:
            raise ValueError, "No output file specified." 
        return out_filenames

    def _get_result_paths(self,data):
        
        result = {}
        result['Info'] = ResultPath(Path=self._info_out_filename(),
                                            IsWritten=True)
        if self.Parameters['-k'].isOn():
            result['Bootstrap'] = ResultPath(
                            Path=self._result_bootstrap_out_filename(),
                            IsWritten=True)
        else:    
            result['Log'] = ResultPath(Path=self._log_out_filename(),
                                            IsWritten=True)
            result['ParsimonyTree'] = ResultPath(
                                      Path=self._parsimony_tree_out_filename(),
                                      IsWritten=True)
            result['Result'] = ResultPath(
                            Path=self._result_tree_out_filename(),
                            IsWritten=True)

        for checkpoint_file in self._checkpoint_out_filenames():
            checkpoint_num = checkpoint_file.split(".")[-1]
            try:
                checkpoint_num = int(checkpoint_num)
            except Exception, e:
                raise ValueError, "%s does not appear to be a valid checkpoint file"
            result['Checkpoint%d' % checkpoint_num] = ResultPath(
                        Path=checkpoint_file,
                        IsWritten=True)
 
        return result


#SOME FUNCTIONS TO EXECUTE THE MOST COMMON TASKS
def raxml_alignment(align_obj,
                 raxml_model="GTRCAT",
                 params={},
                 SuppressStderr=True,
                 SuppressStdout=True):
    """Run raxml on alignment object 

    align_obj: Alignment object
    params: you can set any params except -w and -n

    returns: tuple (phylonode, 
                    parsimonyphylonode, 
                    log likelihood, 
                    total exec time)
    """

    # generate temp filename for output
    params["-w"] = "/tmp/"
    params["-n"] = get_tmp_filename().split("/")[-1]
    params["-m"] = raxml_model
    ih = '_input_as_multiline_string'
    seqs, align_map = align_obj.toPhylip()
    
    #print params["-n"]

    # set up command
    raxml_app = Raxml(
                   params=params,
                   InputHandler=ih,
                   WorkingDir=None,
                   SuppressStderr=SuppressStderr,
                   SuppressStdout=SuppressStdout)

    # run raxml
    ra = raxml_app(seqs)

    # generate tree
    tree_node =  DndParser(ra["Result"])

    # generate parsimony tree
    parsimony_tree_node =  DndParser(ra["ParsimonyTree"])

    # extract log likelihood from log file
    log_file = ra["Log"]
    total_exec_time = exec_time = log_likelihood = 0.0
    for line in log_file:
        exec_time, log_likelihood = map(float, line.split())
        total_exec_time += exec_time

    # remove output files
    ra.cleanUp()

    return tree_node, parsimony_tree_node, log_likelihood, total_exec_time

def build_tree_from_alignment(aln, moltype, best_tree=False, params={}):
    """Returns a tree from Alignment object aln.
    
    aln: an xxx.Alignment object, or data that can be used to build one.
    
    moltype: cogent.core.moltype.MolType object

    best_tree: best_tree suppport is currently not implemented
    
    params: dict of parameters to pass in to the RAxML app controller.
    
    The result will be an xxx.Alignment object, or None if tree fails.
    """
    if best_tree:
        raise NotImplementedError

    if '-m' not in params:
        if moltype == DNA or moltype == RNA:
            params["-m"] = 'GTRMIX'
        elif moltype == PROTEIN:
            params["-m"] = 'PROTMIXGTR'
        else:
            raise ValueError, "Moltype must be either DNA, RNA, or PROTEIN"

    if not hasattr(aln, 'toPhylip'):
        aln = Alignment(aln)
    seqs, align_map = aln.toPhylip()

    # generate temp filename for output    
    params["-w"] = "/tmp/"    
    params["-n"] = get_tmp_filename().split("/")[-1]
    params["-k"] = True
    params["-x"] = randint(1,100000)
    
    ih = '_input_as_multiline_string'    

    raxml_app = Raxml(params=params,
                      InputHandler=ih,
                      WorkingDir=None,
                      SuppressStderr=True,
                      SuppressStdout=True)
    
    raxml_result = raxml_app(seqs)

    tree = DndParser(raxml_result['Bootstrap'], constructor=PhyloNode)
    
    for node in tree.tips():
        node.Name = align_map[node.Name]

    raxml_result.cleanUp()

    return tree