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#!/usr/bin/env python
"""Application controller for FastTree v1.0"""
from cogent.app.parameters import ValuedParameter, FlagParameter
from cogent.app.util import CommandLineApplication, FilePath, system, \
CommandLineAppResult, ResultPath, remove, ApplicationError
from cogent.core.tree import PhyloNode
from cogent.parse.tree import DndParser
from cogent.core.moltype import DNA, RNA, PROTEIN
__author__ = "Daniel McDonald"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Daniel McDonald"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Daniel McDonald"
__email__ = "mcdonadt@colorado.edu"
__status__ = "Development"
class FastTree(CommandLineApplication):
"""FastTree application Controller"""
_command = 'fasttree'
_input_handler = '_input_as_multiline_string'
_parameters = {
'-quiet':FlagParameter('-',Name='quiet'),
'-boot':ValuedParameter('-',Delimiter=' ',Name='boot'),
'-seed':ValuedParameter('-',Delimiter=' ',Name='seed'),
'-nni':ValuedParameter('-',Delimiter=' ',Name='nni'),
'-slow':FlagParameter('-',Name='slow'),
'-fastest':FlagParameter('-',Name='fastest'),
'-top':FlagParameter('-',Name='top'),
'-notop':FlagParameter('-',Name='notop'),
'-topm':ValuedParameter('-',Delimiter=' ',Name='topm'),
'-close':ValuedParameter('-',Delimiter=' ',Name='close'),
'-refresh':ValuedParameter('-',Delimiter=' ',Name='refresh'),
'-matrix':ValuedParameter('-',Delimiter=' ',Name='matrix'),
'-nomatrix':FlagParameter('-',Name='nomatrix'),
'-nj':FlagParameter('-',Name='nj'),
'-bionj':FlagParameter('-',Name='bionj'),
'-nt':FlagParameter('-',Name='nt'),
'-n':ValuedParameter('-',Delimiter=' ',Name='n')}
#FastTree [-quiet] [-boot 1000] [-seed 1253] [-nni 10] [-slow | -fastest]
# [-top | -notop] [-topm 1.0 [-close 0.75] [-refresh 0.8]]
# [-matrix Matrix | -nomatrix] [-nj | -bionj]
# [-nt] [-n 100] [alignment] > newick_tree
def __call__(self,data=None, remove_tmp=True):
"""Run the application with the specified kwargs on data
data: anything that can be cast into a string or written out to
a file. Usually either a list of things or a single string or
number. input_handler will be called on this data before it
is passed as part of the command-line argument, so by creating
your own input handlers you can customize what kind of data
you want your application to accept
remove_tmp: if True, removes tmp files
NOTE: Override of the base class to handle redirected output
"""
input_handler = self.InputHandler
suppress_stderr = self.SuppressStderr
outfile = self.getTmpFilename(self.TmpDir)
self._outfile = outfile
if suppress_stderr:
errfile = FilePath('/dev/null')
else:
errfile = FilePath(self.getTmpFilename(self.TmpDir))
if data is None:
input_arg = ''
else:
input_arg = getattr(self,input_handler)(data)
# Build up the command, consisting of a BaseCommand followed by
# input and output (file) specifications
command = self._command_delimiter.join(filter(None,\
[self.BaseCommand,str(input_arg),'>',str(outfile),'2>',\
str(errfile)]))
if self.HaltExec:
raise AssertionError, "Halted exec with command:\n" + command
# The return value of system is a 16-bit number containing the signal
# number that killed the process, and then the exit status.
# We only want to keep the exit status so do a right bitwise shift to
# get rid of the signal number byte
exit_status = system(command) >> 8
# Determine if error should be raised due to exit status of
# appliciation
if not self._accept_exit_status(exit_status):
raise ApplicationError, \
'Unacceptable application exit status: %s, command: %s'\
% (str(exit_status),command)
out = open(outfile,"r")
err = None
if not suppress_stderr:
err = open(errfile,"r")
result = CommandLineAppResult(out,err,exit_status,\
result_paths=self._get_result_paths(data))
# Clean up the input file if one was created
if remove_tmp:
if self._input_filename:
remove(self._input_filename)
self._input_filename = None
return result
def _get_result_paths(self, data):
result = {}
result['Tree'] = ResultPath(Path=self._outfile)
return result
def build_tree_from_alignment(aln, moltype, best_tree=False, params=None):
"""Returns a tree from alignment
Will check MolType of aln object
"""
if params is None:
params = {}
if moltype == DNA or moltype == RNA:
params['-nt'] = True
elif moltype == PROTEIN:
params['-nt'] = False
else:
raise ValueError, \
"FastTree does not support moltype: %s" % moltype.label
app = FastTree(params=params)
if best_tree:
raise NotImplementedError, "best_tree not implemented yet"
result = app(aln.toFasta())
tree = DndParser(result['Tree'].read(), constructor=PhyloNode)
return tree
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