allpy: bf873e4054c2 allpy/util.py

allpy

view allpy/util.py @ 894:bf873e4054c2

test: add make rule alignments, downloading simple alignment This alignment is similar to alignment 1jcc_in.fasta, removed in [d1a3d3ee0843]. It consists of almost identical sequences of two proteins with resolved structure.

author	Boris Nagaev <bnagaev@gmail.com>
date	Fri, 23 Sep 2011 14:00:34 +0400
parents	4fa7b10ce252
children	7b2a37ff1662

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