allpy: 19ffcf1ac4a0 allpy/util.py

allpy

view allpy/util.py @ 935:19ffcf1ac4a0

Fixed bug in processors: used Block class for reading alignment file. Until recent changes (introduction of Alignment/Block._append_columns) it worked out fine. But practically, we used alignment API: we created an empty object and called append_file on it. For blocks this resulted in a block that did not know it's alignment. Recent changes in implementation caused blocks to actually have their own specific methods besides constructor, and these methods use knowlege of alignment a block belongs to. Hence, the previous behaviour was a bug.

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Mon, 28 Nov 2011 18:33:25 +0300
parents	7b2a37ff1662
children	08d892230e8c 87ba56d634cf

line source

1 """Miscellanous utilities.

2 """

3 import sys

4 import warnings

6 def unzip(seq):

7 """The oppozite of zip() builtin."""

8 a, b = [], []

9 for x, y in seq:

10 a.append(x)

11 b.append(y)

12 return a, b

14 def open(filename, mode='r'):

15 """Open file. Return stdin/stdout for filename '-'."""

16 if filename == '-':

17 if 'w' in mode or 'a' in mode or '+' in mode:

18 return sys.stdout

19 if 'r' in mode:

20 return sys.stdin

21 raise AssertionError("Unknown file mode: %s" % mode)

22 else:

23 return file(filename, mode)

25 def remove_each(string, substrings):

26 """Remove each of substrings from string."""

27 for sub in substrings:

28 string = string.replace(sub, "")

29 return string

31 class UserDict(dict):

32 """Clone of dict that user may add attributes to."""

33 pass

35 class UserList(list):

36 """Clone of list that user may add attributes to."""

37 pass

39 class UserString(str):

40 """Clone of str that user may add attributes to."""

41 pass

43 def deprecated(message):

44 """Warn about function being deprecated."""

45 warnings.warn(message, DeprecationWarning, stacklevel=2)

47 class lazy_import(object):

48 """Lazy module import to help breaking bad import loops."""

49 def __init__(self, name, globals={}, locals={}, fromlist=[], level=-1):

50 self.name = name

51 self.globals = globals

52 self.locals = locals

53 self.fromlist = fromlist

54 self.level = level

55 def __getattr__(self, attr):

56 self.module = __import__(

57 self.name, self.globals, self.locals, self.fromlist, self.level

58 )

59 self.__dict__ = self.module.__dict__

60 return self.__dict__[attr]

62 class Binder(object):

63 def __init__(self, func, *args, **kwargs):

64 self.func = func

65 self.args = args

66 self.kwargs = kwargs

67 def __call__(self):

68 try:

69 self.func(*self.args, **self.kwargs)

70 except Exception, e:

71 sys.stderr.write("%s: %s\n" % (e.__class__, e))

73 # vim: set et ts=4 sts=4 sw=4: