#!/usr/bin/env python
"""Application controller for pplacer 1.1"""
__author__ = "Kyle Bittinger"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Kyle Bittinger","Jesse Stombaugh"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Kyle Bittinger"
__email__ = "kylebittinger@gmail.com"
__status__ = "Production"
from cogent.app.parameters import ValuedParameter, FlagParameter
from cogent.app.util import CommandLineApplication, FilePath, system, \
CommandLineAppResult, ResultPath, remove, ApplicationError, \
get_tmp_filename
from cogent.core.alignment import Alignment
from cogent.app.guppy import build_tree_from_json_using_params
from os.path import splitext,abspath,join,split
from StringIO import StringIO
from cogent.parse.phylip import get_align_for_phylip
from cogent.parse.tree import DndParser
from cogent.core.tree import PhyloNode
class Pplacer(CommandLineApplication):
"""pplacer Application Controller
"""
_command = 'pplacer'
_input_handler = '_input_as_multiline_string'
_parameters = {
# -c Specify the path to the reference package.
'-c': ValuedParameter('-', Name='c', Delimiter=' ', IsPath=True),
# -t Specify the reference tree filename.
'-t': ValuedParameter('-', Name='t', Delimiter=' ', IsPath=True),
# -r Specify the reference alignment filename.
'-r': ValuedParameter('-', Name='r', Delimiter=' ', IsPath=True),
# -s Supply a phyml stats.txt or a RAxML info file giving the model parameters.
'-s': ValuedParameter('-', Name='s', Delimiter=' ', IsPath=True),
# -d Specify the directory containing the reference information.
'-d': ValuedParameter('-', Name='d', Delimiter=' ', IsPath=True),
# -p Calculate posterior probabilities.
'-p': FlagParameter('-', Name='p'),
# -m Substitution model. Protein: are LG, WAG, or JTT. Nucleotides: GTR.
'-m': ValuedParameter('-', Name='m', Delimiter=' '),
# --model-freqs Use model frequencies instead of reference alignment frequencies.
'--model-freqs': FlagParameter('--', Name='model-freqs'),
# --gamma-cats Number of categories for discrete gamma model.
'--gamma-cats': ValuedParameter('--', Name='gamma-cats', Delimiter=' '),
# --gamma-alpha Specify the shape parameter for a discrete gamma model.
'--gamma-alpha': ValuedParameter('--', Name='gamma-alpha', Delimiter=' '),
# --ml-tolerance 1st stage branch len optimization tolerance (2nd stage to 1e-5). Default: 0.01.
'--ml-tolerance': ValuedParameter('--', Name='ml-tolerance', Delimiter=' '),
# --pp-rel-err Relative error for the posterior probability calculation. Default is 0.01.
'--pp-rel-err': ValuedParameter('--', Name='pp-rel-err', Delimiter=' '),
# --unif-prior Use a uniform prior rather than exponential.
'--unif-prior': FlagParameter('--', Name='unif-prior'),
# --start-pend Starting pendant branch length. Default is 0.1.
'--start-pend': ValuedParameter('--', Name='start-pend', Delimiter=' '),
# --max-pend Set the maximum ML pendant branch length. Default is 2.
'--max-pend': ValuedParameter('--', Name='max-pend', Delimiter=' '),
# --max-strikes Maximum number of strikes for baseball. 0 -> no ball playing. Default is 6.
'--max-strikes': ValuedParameter('--', Name='max-strikes', Delimiter=' '),
# --strike-box Set the size of the strike box in log likelihood units. Default is 3.
'--strike-box': ValuedParameter('--', Name='strike-box', Delimiter=' '),
# --max-pitches Set the maximum number of pitches for baseball. Default is 40.
'--max-pitches': ValuedParameter('--', Name='max-pitches', Delimiter=' '),
# --fantasy Desired likelihood cutoff for fantasy baseball mode. 0 -> no fantasy.
'--fantasy': ValuedParameter('--', Name='fantasy', Delimiter=' '),
# --fantasy-frac Fraction of fragments to use when running fantasy baseball. Default is 0.1.
'--fantasy-frac': ValuedParameter('--', Name='fantasy-frac', Delimiter=' '),
# --write-masked Write alignment masked to the region without gaps in the query.
'--write-masked': FlagParameter('--', Name='write-masked'),
# --verbosity Set verbosity level. 0 is silent, and 2 is quite a lot. Default is 1.
'--verbosity': ValuedParameter('--', Name='verbosity', Delimiter=' '),
# --unfriendly Do not run friend finder pre-analysis.
'--unfriendly': FlagParameter('--', Name='unfriendly'),
# --out-dir Specify the directory to write place files to.
'--out-dir': ValuedParameter('--', Name='out-dir', Delimiter=' ', IsPath=True),
# --pretend Only check out the files then report. Do not run the analysis.
'--pretend': FlagParameter('--', Name='pretend'),
# --csv Make a CSV file with the results.
'--csv': FlagParameter('--', Name='csv'),
# --old-format Make an old-format placefile with the resuls.
'--old-format': FlagParameter('--', Name='old-format'),
# --diagnostic Write file describing the 'diagnostic' mutations for various clades.
'--diagnostic': FlagParameter('--', Name='diagnostic'),
# --check-like Write out the likelihood of the reference tree, calculated two ways.
'--check-like': FlagParameter('--', Name='check-like'),
# --version Write out the version number and exit.
'--version': FlagParameter('--', Name='version'),
# --help Display this list of options
'--help': FlagParameter('--', Name='help'),
}
def getTmpFilename(self, tmp_dir="/tmp",prefix='tmp',suffix='.fasta',\
include_class_id=False,result_constructor=FilePath):
""" Define Tmp filename to contain .fasta suffix, since pplacer requires
the suffix to be .fasta """
return super(Pplacer,self).getTmpFilename(tmp_dir=tmp_dir,
prefix=prefix,
suffix=suffix,
include_class_id=include_class_id,
result_constructor=result_constructor)
def _handle_app_result_build_failure(self,out,err,exit_status,result_paths):
""" Catch the error when files are not produced """
raise ApplicationError, \
'Pplacer failed to produce an output file due to the following error: \n\n%s ' \
% out.read()
def _get_result_paths(self,data):
""" Define the output filepaths """
output_dir = self.Parameters['--out-dir'].Value
result = {}
result['json'] = ResultPath(Path=join(output_dir,
splitext(split(self._input_filename)[-1])[0] + \
'.jplace'))
return result
def insert_sequences_into_tree(aln, moltype, params={},
write_log=True):
"""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
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.
"""
# convert aln to phy since seq_names need fixed to run through pplacer
new_aln=get_align_for_phylip(StringIO(aln))
# convert aln to fasta in case it is not already a fasta file
aln2 = Alignment(new_aln)
seqs = aln2.toFasta()
ih = '_input_as_multiline_string'
pplacer_app = Pplacer(params=params,
InputHandler=ih,
WorkingDir=None,
SuppressStderr=False,
SuppressStdout=False)
pplacer_result = pplacer_app(seqs)
# write a log file
if write_log:
log_fp = join(params["--out-dir"],'log_pplacer_' + \
split(get_tmp_filename())[-1])
log_file=open(log_fp,'w')
log_file.write(pplacer_result['StdOut'].read())
log_file.close()
# use guppy to convert json file into a placement tree
guppy_params={'tog':None}
new_tree=build_tree_from_json_using_params(pplacer_result['json'].name, \
output_dir=params['--out-dir'], \
params=guppy_params)
pplacer_result.cleanUp()
return new_tree
