allpy: cfcbd13f6761 allpy/util.py

allpy

view allpy/util.py @ 864:cfcbd13f6761

Added fileio.BioPythonFile as a method to parse unknown file formats [closes #106] Biopython can parse more formats than EMBOSS, but surprisingly, it cannot do msf. Also, there is no way to see in the current tests, where a test used biopython or emboss for a particular IO task. This will likely be fixed with the 1.5.0 release with the new fileio system. For now, Biopython has precedence over EMBOSS, so an IO test of msf tests EMBOSS, and IO test of Stockholm tests Biopython.

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Mon, 25 Jul 2011 14:40:41 +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: