/usr/share/pyshared/cogent/app/stride.py is in python-cogent 1.5.3-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | #!/usr/bin/env python
"""Application controller for stride."""
try:
from cStringIO import StringIO
except ImportError:
from StringIO import StringIO
from cogent.struct.selection import einput
from cogent.parse.stride import stride_parser
from cogent.struct.annotation import xtradata
from cogent.app.util import CommandLineApplication, ResultPath
from cogent.app.parameters import FlagParameter, ValuedParameter
from cogent.format.pdb import PDBWriter
__author__ = "Marcin Cieslik"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__contributors__ = ["Marcin Cieslik"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Marcin Cieslik"
__email__ = "mpc4p@virginia.edu"
__status__ = "Development"
class Stride(CommandLineApplication):
"""Application controller for stride."""
_parameters = {
# report hydrogen bonds
'-h':FlagParameter(Prefix='-', Name='h', Value=False),
# calculate contact order
'-k':FlagParameter(Prefix='-', Name='k', Value=False),
# print out the contact map only
'-w':FlagParameter(Prefix='-', Name='w', Value=False),
# write output as file
'-f':ValuedParameter(Prefix='-', Name='f', Delimiter=''),
# write output as molscript file
'-m':ValuedParameter(Prefix='-', Name='m', Delimiter=''),
}
_command = "stride"
_input_handler = '_input_as_multiline_string'
def _input_as_multiline_string(self, data):
"""This allows to feed entities to stride."""
dummy_file = StringIO()
PDBWriter(dummy_file, data)
dummy_file.seek(0)
data = super(Stride, self)._input_as_multiline_string(dummy_file.read())
return data
def _align_out_filename(self):
if self.Parameters['-f'].isOn():
aln_filename = self._absolute(str(self.Parameters['-f'].Value))
else:
aln_filename = None
return aln_filename
def _get_result_paths(self, data):
result = {}
if self.Parameters['-f'].isOn():
out_name = self._align_out_filename()
result['File'] = ResultPath(Path=out_name, IsWritten=True)
return result
def stride_xtra(entities, **kwargs):
"""Runs the stride application and maps the result on the residue xtra
dictionaries.
"""
structures = einput(entities, 'S')
if len(structures.values()) > 1:
raise ValueError('Entities from multiple structures are not supported.')
stride_app = Stride(**kwargs)
result = stride_app(entities)['StdOut'].readlines()
result = stride_parser(result)
xtradata(result, structures.values()[0][(0,)])
return result
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