/usr/lib/python2.7/dist-packages/cogent/app/nupack.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 | #!/usr/bin/env python
"""Application controller for NUPACK v1.2 application
"""
import shutil
from os import remove, system, environ
from cogent.app.util import CommandLineApplication,\
CommandLineAppResult, ResultPath, FilePath, ApplicationError
from cogent.app.parameters import Parameter, FlagParameter, ValuedParameter,\
MixedParameter,Parameters, _find_synonym, is_not_None
__author__ = "Shandy Wikman"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__contributors__ = ["Shandy Wikman"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Shandy Wikman"
__email__ = "ens01svn@cs.umu.se"
__status__ = "Development"
if 'NUPACK_DATA' not in environ:
raise RuntimeError, \
'NUPACK app controller requires the NUPACK_DATA environment variable'
nupack_data_dir = environ['NUPACK_DATA']
nupack_data_dna = 'dataS_G.dna'
nupack_data_rna = 'dataS_G.rna'
class Nupack(CommandLineApplication):
"""Application controller for Nupack_1.2 application
Predicts RNA secondary structure
All pseudoknot-free secondary structures are allowed, as well as simple
pseudoknots.
"""
_command = 'Fold.out'
_input_handler = '_input_as_string'
def _input_as_lines(self,data):
""" Write a seq of lines to a temp file and return the filename string
data: a sequence to be written to a file, each element of the
sequence will compose a line in the file
Note: '\n' will be stripped off the end of each sequence element
before writing to a file in order to avoid multiple new lines
accidentally be written to a file
"""
filename = self._input_filename = self.getTmpFilename(self.WorkingDir)
data_file = open(filename,'w')
data_to_file = '\n'.join([str(d).strip('\n') for d in data])
data_file.write(data_to_file)
data_file.write('\n') #needs a new line att the end of input
data_file.close()
return filename
def _get_result_paths(self,data):
"""Return a dict of ResultPath objects representing all possible output
This dictionary will have keys based
on the name that you'd like to access the file by in the
CommandLineAppResult object that will be created, and the values
which are ResultPath objects.
"""
result = {}
try:
f = open((self.WorkingDir+'out.pair'))
f.close()
result['pair'] =\
ResultPath(Path=(self.WorkingDir+'out.pair'))
except IOError:
pass
try:
f = open((self.WorkingDir+'out.ene'))
f.close()
result['ene'] =\
ResultPath(Path=(self.WorkingDir+'out.ene'))
except IOError:
pass
return result
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
"""
input_handler = self.InputHandler
suppress_stdout = self.SuppressStdout
suppress_stderr = self.SuppressStderr
if suppress_stdout:
outfile = FilePath('/dev/null')
else:
outfile = self.getTmpFilename(self.TmpDir)
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
# copy over data files
nupack_data_dna_src = '/'.join([nupack_data_dir, nupack_data_dna])
nupack_data_rna_src = '/'.join([nupack_data_dir, nupack_data_rna])
shutil.copy(nupack_data_dna_src, self.WorkingDir)
shutil.copy(nupack_data_rna_src, self.WorkingDir)
# 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
# NOTE: we copy the data files to the working directory first
exit_status = system(command) >> 8
# remove data files
nupack_data_dna_dst = ''.join([self.WorkingDir, nupack_data_dna])
nupack_data_rna_dst = ''.join([self.WorkingDir, nupack_data_rna])
remove(nupack_data_dna_dst)
remove(nupack_data_rna_dst)
# 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)
# open the stdout and stderr if not being suppressed
out = None
if not suppress_stdout:
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
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