/usr/lib/python2.7/dist-packages/cogent/app/guppy.py is in python-cogent 1.9-9.
This file is owned by root:root, with mode 0o644.
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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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 | #!/usr/bin/env python
"""Application controller for guppy 1.1"""
__author__ = "Jesse Stombaugh"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Jesse Stombaugh"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Jesse Stombaugh"
__email__ = "jesse.stombaugh@colorado.edu"
__status__ = "Production"
from cogent.app.parameters import ValuedParameter, FlagParameter
from cogent.app.util import CommandLineApplication, FilePath, system, \
CommandLineAppResult, ResultPath, remove, ApplicationError
from cogent.core.alignment import Alignment
from os.path import splitext,split,join
from os import listdir
from cogent.parse.tree import DndParser
from cogent.core.tree import PhyloNode
class Guppy(CommandLineApplication):
"""guppy Application Controller
"""
_command = 'guppy'
_input_handler = '_input_as_multiline_string'
_parameters = {
#visualizations
# makes trees with edges fattened in proportion to the number of reads
'fat': FlagParameter('', Name='fat'),
# maps an an arbitrary vector of the correct length to the tree
'heat': FlagParameter('', Name='heat'),
# writes a taxonomically annotated reference tree and an induced
# taxonomic tree
'ref_tree': FlagParameter('', Name='ref_tree'),
# makes one tree for each query sequence, showing uncertainty
'sing': FlagParameter('', Name='sing'),
# makes a tree with each of the reads represented as a pendant edge
'tog': FlagParameter('', Name='tog'),
#statistical comparison
# draws the barycenter of a placement collection on the reference tree
'bary': FlagParameter('', Name='bary'),
# makes a phyloXML tree showing the bootstrap values
'bootviz': FlagParameter('', Name='bootviz'),
# calculates the EDPL uncertainty values for a collection of pqueries
'edpl': FlagParameter('', Name='edpl'),
# calculates the Kantorovich-Rubinstein distance and corresponding
# p-values
'kr': FlagParameter('', Name='kr'),
# makes a heat tree
'kr_heat': FlagParameter('', Name='kr_heat'),
# performs edge principal components
'pca': FlagParameter('', Name='pca'),
# writes out differences of masses for the splits of the tree
'splitify': FlagParameter('', Name='splitify'),
# performs squash clustering
'squash': FlagParameter('', Name='squash'),
#classification
# outputs classification information in a tabular or SQLite format
'classify': FlagParameter('', Name='classify'),
#utilities
# check a reference package
'check_refpkg': FlagParameter('', Name='check_refpkg'),
# splits apart placements with multiplicity, undoing a round procedure
'demulti': FlagParameter('', Name='demulti'),
# prints out a pairwise distance matrix between the edges
'distmat': FlagParameter('', Name='distmat'),
# filters one or more placefiles by placement name
'filter': FlagParameter('', Name='filter'),
# writes the number of leaves of the reference tree and the number of
# pqueries
'info': FlagParameter('', Name='info'),
# merges placefiles together
'merge': FlagParameter('', Name='merge'),
# restores duplicates to deduped placefiles
'redup': FlagParameter('', Name='redup'),
# clusters the placements by rounding branch lengths
'round': FlagParameter('', Name='round'),
# makes SQL enabling taxonomic querying of placement results
'taxtable': FlagParameter('', Name='taxtable'),
# converts old-style .place files to .json placement files
'to_json': FlagParameter('', Name='to_json'),
# Run the provided batch file of guppy commands
'batch': FlagParameter('--', Name='batch'),
# Print version and exit
'version': FlagParameter('--', Name='version'),
# Print a list of the available commands.
'cmds': FlagParameter('--', Name='cmds'),
# Display this list of options
'--help': FlagParameter('--', Name='help'),
# Display this list of options
'-help': FlagParameter('-', Name='help'),
}
def getTmpFilename(self, tmp_dir='/tmp/',prefix='tmp',suffix='.json',\
include_class_id=False,result_constructor=FilePath):
""" Define Tmp filename to contain .json suffix, since guppy requires
the suffix to be .json """
return super(Guppy,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, \
'Guppy failed to produce an output file due to the following error: \n\n%s ' \
% err.read()
def _get_result_paths(self,data):
basepath,basename=split(splitext(self._input_filename)[0])
outfile_list=listdir(split(self._input_filename)[0])
result = {}
for i in outfile_list:
if i.startswith(basename) and not i.endswith('.json') and \
not i.endswith('.txt'):
result['result'] = ResultPath(Path=join(basepath,i))
return result
def build_tree_from_json_using_params(fname,output_dir='/tmp/',params={}):
"""Returns a tree from a json.
fname: filepath to input json
output_dir: location of output files
params: dict of parameters to pass in to the RAxML app controller.
The result will be a Tree.
"""
# convert aln to fasta in case it is not already a fasta file
ih = '_input_as_multiline_string'
guppy_app = Guppy(params=params,
InputHandler=ih,
WorkingDir=output_dir,
TmpDir=output_dir,
SuppressStderr=True,
SuppressStdout=True,
HALT_EXEC=False)
guppy_result = guppy_app(open(fname).read())
try:
new_tree=guppy_result['result'].read()
except:
# catch the error of not producing any results and print the command
# run so user can check error
guppy_cmd=Guppy(params=params,
InputHandler=ih,
WorkingDir=output_dir,
TmpDir=output_dir,
SuppressStderr=True,
SuppressStdout=True,
HALT_EXEC=True)
out_msg=guppy_cmd(open(fname).read())
tree = DndParser(new_tree, constructor=PhyloNode)
guppy_result.cleanUp()
return tree
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