/usr/lib/python2.7/dist-packages/macsypy/registries.py is in macsyfinder 1.0.2-3.
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 | # -*- coding: utf-8 -*-
################################################################################
# MacSyFinder - Detection of macromolecular systems in protein datasets #
# using systems modelling and similarity search. #
# Authors: Sophie Abby, Bertrand Néron #
# Copyright © 2014 Institut Pasteur (Paris) and CNRS. #
# See the COPYRIGHT file for details #
# #
# MacsyFinder is distributed under the terms of the GNU General Public License #
# (GPLv3). See the COPYING file for details. #
################################################################################
import os
import glob
_prefix_data = '/usr/share/macsyfinder'
if 'MACSY_HOME' in os.environ and os.environ['MACSY_HOME']:
_prefix_data = os.path.join(os.environ['MACSY_HOME'], 'data')
class ProfilesRegistry(object):
"""
ProfilesRegistry register all profiles available.
"""
def __init__(self, cfg):
"""
get all profiles available in global macsyfinder share data location (depending installation /usr/share/data/profile)
and overload it with the location specify in the macsyfinder configuration (either in config file or command line)
:param cfg: the macsyfinder configuration
:type cfg: :class:`macsypy.config.Config` object
"""
self._register = {}
global_path = os.path.join(_prefix_data, 'macsyfinder' , 'profiles')
self._fill_profile(global_path , cfg)
local_path = cfg.profile_dir
if local_path:
self._fill_profile(local_path, cfg)
def _fill_profile(self, dir_path, cfg):
for path in glob.glob(os.path.join(dir_path, '*' + cfg.profile_suffix)):
name = os.path.basename(path)
name = name[:-1 * len(cfg.profile_suffix)]
self._register[name] = path
def __getattr__(self, name):
return getattr(self._register, name)
class DefinitionsRegistry(object):
"""
DefinitionsRegistry register all definition systems available.
"""
def __init__(self, cfg):
"""
get all systems defitions available in global macsyfinder share data location ( depending installation /usr/share/data/DEF)
and overload it with the location specify in the macsyfinder configuration (either in config file or command line)
:param cfg: the macsyfinder configuration
:type cfg: :class:`macsypy.config.Config` object
"""
self._register = {}
global_path = os.path.join(_prefix_data, 'macsyfinder' , 'DEF')
self._fill_def(global_path)
local_path = cfg.def_dir
if local_path:
self._fill_def(local_path)
def _fill_def(self, dir_path):
for path in glob.glob(os.path.join(dir_path, '*.xml')):
name = os.path.basename(path)
name = os.path.splitext(name)[0]
self._register[name] = path
def __getattr__(self, name):
return getattr(self._register, name)
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