/usr/share/pyshared/cogent/app/fasttree.py is in python-cogent 1.5.3-2.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 | #!/usr/bin/env python
"""Application controller for FastTree
designed for FastTree v1.1.0 . Also functions with v2.0.1, v2.1.0, and v2.1.3
though only with basic functionality"""
from cogent.app.parameters import ValuedParameter, FlagParameter, \
MixedParameter
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
from cogent.core.alignment import SequenceCollection
__author__ = "Daniel McDonald"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Daniel McDonald", "Justin Kuczynski"]
__license__ = "GPL"
__version__ = "1.5.3"
__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'),
'-pseudo':MixedParameter('-',Delimiter=' ', Name='pseudo'),
'-intree':ValuedParameter('-',Delimiter=' ',Name='intree'),
'-spr':ValuedParameter('-',Delimiter=' ',Name='spr'),
'-constraints':ValuedParameter('-',Delimiter=' ',\
Name='constraints'),
'-constraintWeight':ValuedParameter('-',Delimiter=' ',\
Name='constraintWeight'),\
'-makematrix':ValuedParameter('-',Delimiter=' ',Name='makematrix')}
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
if best_tree:
params['-slow'] = True
#Create mapping between abbreviated IDs and full IDs
int_map, int_keys = aln.getIntMap()
#Create SequenceCollection from int_map.
int_map = SequenceCollection(int_map,MolType=moltype)
app = FastTree(params=params)
result = app(int_map.toFasta())
tree = DndParser(result['Tree'].read(), constructor=PhyloNode)
#remap tip names
for tip in tree.tips():
tip.Name = int_keys[tip.Name]
return tree
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