# Copyright (c) 2005 Gavin E. Crooks # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # """Extra utilities and core classes not in standard python. """ # private submodules, such as _which, are for internal corebio use. from __future__ import absolute_import __all__ = ('isblank', 'isfloat', 'isint', 'fcmp', 'remove_whitespace', 'invert_dict', 'update', 'stdrepr', 'Token', 'Struct', 'Reiterate', 'deoptparse', 'crc32', 'crc64', 'FileIndex', 'find_command', 'ArgumentError', 'frozendict','group_count', 'resource_string', 'resource_stream','resource_filename') import os.path import math try : import pkg_resources except ImportError : pkg_resources = None from .._py3k import iteritems def isblank( string) : """Is this whitespace or an empty string?""" if string == '' : return True return string.isspace() def isfloat(s): """Does this object represent a floating point number? """ try: float(s) return True except (ValueError, TypeError): return False def isint(s): """Does this object represent an integer?""" try: int(s) return True except (ValueError, TypeError): return False def fcmp(x, y, precision): """Floating point comparison.""" # TODO: Doc string, default precision. Test if math.fabs(x-y) < precision: return 0 elif x < y: return -1 return 1 def remove_whitespace( astring) : """Remove all whitespace from a string.""" # TODO: Is this horrible slow? return "".join(astring.split()) def invert_dict( dictionary) : """Constructs a new dictionary with inverted mappings so that keys become values and vice versa. If the values of the original dictionary are not unique then only one of the original keys will be included in the new dictionary. """ return dict((value, key) for key, value in iteritems(dictionary)) def update(obj, **entries): """Update an instance with new values. >>> update({'a': 1}, a=10, b=20) {'a': 10, 'b': 20} """ if hasattr(obj, 'update') : obj.update(entries) else: for k, v in iteritems(entries): setattr(obj, k, v) return obj def stdrepr( obj, attributes=None, name=None) : """Create a standard representation of an object.""" if name==None : name = obj.__class__.__name__ if attributes==None: attributes = obj.__class__.__slots__ args = [] for a in attributes : if a[0]=='_' : continue args.append( '%s=%s' % ( a, repr( getattr(obj, a) ) ) ) args = ',\n'.join(args).replace('\n', '\n ') return '%s(\n %s\n)' % (name, args) def group_count(i): """An iteration that returns tuples of items and the number of consecutive occurrences. Thus group_count('aabbbc') yields ('a',2), ('b',3), ('c',1) """ from itertools import groupby return [ (item, sum( 1 for n in group) ) for item, group in groupby(i)] class Token(object): """Represents the items returned by a file scanner, normally processed by a parser. Attributes : o typeof -- a string describing the kind of token o data -- the value of the token o lineno -- the line of the file on which the data was found (if known) o offset -- the offset of the data within the line (if known) """ __slots__ = [ 'typeof', 'data', 'lineno', 'offset'] def __init__(self, typeof, data=None, lineno=-1, offset=-1) : self.typeof = typeof self.data = data self.lineno = lineno self.offset = offset def __repr__(self) : return stdrepr( self) def __str__(self): coord = str(self.lineno) if self.offset != -1 : coord += ':'+str(self.offset) coord = coord.ljust(7) return (coord+ ' '+ self.typeof +' : ').ljust(32)+ str(self.data or '') def Struct(**kwargs) : """Create a new instance of an anonymous class with the supplied attributes and values. >>> s = Struct(a=3,b=4) >>> s Struct( a=3, b=4 ) >>> s.a 3 """ name = 'Struct' def _init(obj, **kwargs): for k, v in iteritems(kwargs): setattr( obj, k, v) def _repr(obj) : return stdrepr( obj, obj.__slots__, name) adict = {} adict['__slots__'] = kwargs.keys() adict['__init__'] = _init adict['__repr__'] = _repr return type( name, (object,) , adict)(**kwargs) class Reiterate(object): """ A flexible wrapper around a simple iterator. """ def __new__(cls, iterator): if isinstance(iterator, cls) : return iterator new = object.__new__(cls) new._iterator = iter(iterator) new._stack = [] new._index = 0 return new def __init__(self, *args, **kw): pass def __iter__(self): return self def __next__(self): """Return the next item in the iteration.""" self._index += 1 if self._stack: return self._stack.pop() else: return next(self._iterator) next = __next__ def index(self) : """The number of items returned. Incremented by next(), decremented by push(), unchanged by peek() """ return self._index def push(self, item) : """Push an item back onto the top of the iterator,""" self._index -=1 self._stack.append(item) def peek(self) : """Returns the next item, but does not advance the iteration. Returns None if no more items. (Bit may also return None as the next item.)""" try : item = next(self) self.push(item) return item except StopIteration: return None def has_item(self) : """More items to return?""" try: item = next(self) self.push(item) return True except StopIteration: return False def filter(self, predicate): """Return the next item in the iteration that satisfied the predicate.""" next_item = next(self) while not predicate(next_item): next_item = next(self) return next_item # End class Reiterate def crc32(string): """Return the standard CRC32 checksum as a hexidecimal string.""" import binascii return "%08X"% binascii.crc32(string.encode()) _crc64_table =None def crc64(string): """ Calculate ISO 3309 standard cyclic redundancy checksum. Used, for example, by SWISS-PROT. Returns : The CRC as a hexadecimal string. Reference: o W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, "Numerical recipes in C", 2nd ed., Cambridge University Press. Pages 896ff. """ # Adapted from biopython, which was adapted from bioperl global _crc64_table if _crc64_table is None : # Initialisation of CRC64 table table = [] for i in range(256): l = i part_h = 0 for j in range(8): rflag = l & 1 l >>= 1 if part_h & 1: l |= (1 << 31) part_h >>= 1 if rflag: part_h ^= 0xd8000000 table.append(part_h) _crc64_table = tuple(table) crcl = 0 crch = 0 for c in string: shr = (crch & 0xFF) << 24 temp1h = crch >> 8 temp1l = (crcl >> 8) | shr idx = (crcl ^ ord(c)) & 0xFF crch = temp1h ^ _crc64_table[idx] crcl = temp1l return "%08X%08X" % (crch, crcl) # End crc64 class FileIndex(object) : """Line based random access to a file. Quickly turn a file into a read-only database. Attr: - indexfile -- The file to be indexed. Can be set to None and latter replaced with a new file handle, for exampel, if you need to close and latter reopen the file. Bugs: User must set the indexedfile to None before pickling this class. """ __slots__ = [ 'indexedfile', '_parser', '_positions', '_keys', '_key_dict'] def __init__(self, indexedfile, linekey = None, parser=None) : """ Args: - indexedfile -- The file to index - linekey -- An optional function. keyofline() will be passed each line of the file in turn and should return a string to index the line, or None. If keyofline() is supplied, then only lines that generate keys are indexed. - parser -- An optional parser. A function that reads from a file handle positioned at the start of a record and returns an object. """ def default_parser(seekedfile) : return seekedfile.readline() if parser is None : parser = default_parser self._parser = parser indexedfile.seek(0) positions = [] keys = [] while True : position = indexedfile.tell() line = indexedfile.readline() if line == '' : break if linekey : k = linekey(line) if k is None: continue keys.append(k) positions.append(position) self.indexedfile = indexedfile self._positions = tuple(positions) if linekey : self._keys = tuple(keys) self._key_dict = dict( zip(keys, positions)) def tell(self, item) : if isinstance(item, str) : p = self._key_dict[item] else : p = self._positions[item] return p def seek(self, item) : """Seek the indexfile to the position of item.""" self.indexedfile.seek(self.tell(item)) def __iter__(self) : for i in range(0, len(self)) : yield self[i] def __len__(self) : return len(self._positions) def __getitem__(self, item) : self.indexedfile.seek(self.tell(item)) return self._parser(self.indexedfile) def __contains__(self, item) : try: self.tell(item) return True except KeyError : return False except IndexError : return False # End class FileIndex def find_command(command, path=None): """Return the full path to the first match of the given command on the path. Arguments: - command -- is a the name of the executable to search for. - path -- is an optional alternate path list to search. The default is to use the COREBIOPATH environment variable, if it exists, else the PATH environment variable. Raises: - EnvironmentError -- If no match is found for the command. By default the COREBIOPATH or PATH environment variable is searched (as well as, on Windows, the AppPaths key in the registry), but a specific 'path' list to search may be specified as well. Author: Adapted from code by Trent Mick (TrentM@ActiveState.com) See: http://trentm.com/projects/which/ """ from . import _which if path is None : path = os.environ.get("COREBIOPATH", "").split(os.pathsep) if path == ['']: path = None try : match = next(_which.whichgen(command, path)) except (StopIteration, _which.WhichError): raise EnvironmentError("Could not find '%s' on the path." % command) return match class ArgumentError(ValueError) : """ A subclass of ValueError raised when a function receives an argument that has the right type but an inappropriate value, and the situation is not described by a more precise exception such as IndexError. The name of the argument or component at fault and (optionally) the value are also stored. """ def __init__(self, message, key, value=None) : """ Args: - msg -- An error message. - key -- The name of the argument or component at fault. - value -- Optional value of the argument. """ ValueError.__init__(self, key, message ) self.msg = message #Changed .message to .msg because of deprecation warning in python 2.6 self.key = key self.value = value # end class ArgumentError class frozendict(dict): """A frozendict is a dictionary that cannot be modified after being created - but it is hashable and may serve as a member of a set or a key in a dictionary. # Author: Adapted from code by Oren Tirosh """ # See: http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/414283 @property def _blocked_attribute(self): raise AttributeError("A frozendict cannot be modified.") __delitem__ = _blocked_attribute __setitem__ = _blocked_attribute clear = _blocked_attribute pop = _blocked_attribute popitem = _blocked_attribute setdefault = _blocked_attribute update = _blocked_attribute def __new__(cls, *args, **kw): new = dict.__new__(cls) dict.__init__(new, *args, **kw) return new def __init__(self, *args, **kw): pass def __hash__(self): try: return self._cached_hash except AttributeError: # Hash keys, not items, since items can be mutable and unhasahble. h = self._cached_hash = hash(tuple(sorted(self.keys()))) return h def __repr__(self): return "frozendict(%s)" % dict.__repr__(self) # end class frozendict def resource_string( modulename, resource, basefilename = None): """Locate and return a resource as a string. >>> f = resource_string( __name__, 'somedatafile', __file__) """ if pkg_resources : return pkg_resources.resource_string(modulename, resource) f = resource_stream( modulename, resource, basefilename) return f.read() def resource_stream( modulename, resource, basefilename = None): """Locate and return a resource as a stream. >>> f = resource_stream( __name__, 'somedatafile', __file__) """ return open( resource_filename( modulename, resource, basefilename) ) def resource_filename( modulename, resource, basefilename = None): """Locate and return a resource filename. >>> f = resource_filename( __name__, 'somedatafile', __file__) A resource is a data file stored with the python code in a package. All three resource methods (resource_string, resource_stream, resource_filename) call the corresponding methods in the 'pkg_resources' module, if installed. Otherwise, we resort to locating the resource in the local filesystem. However, this does not work if the package is located inside a zip file. """ if pkg_resources : return pkg_resources.resource_filename(modulename, resource) if basefilename is None : raise NotImplementedError( "Require either basefilename or pkg_resources") return os.path.join(os.path.dirname(basefilename), resource)