allpy: ca0b757452da allpy/util.py

allpy

view allpy/util.py @ 1096:ca0b757452da

Added meta-processor `FixNamesAndOrder`; called from `Needle` and `Muscle` (closes #134) Processors `Needle()` and `Muscle()` now can deal with all kinds of stuff in sequence names: spaces, colons, duplicate sequence names. For readers of #134: please note, that this commit actually does exactly __nothing__ with `ExternalCommand` processor itself, rather adds a new meta-processor to be applied to it or any other processor.

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Sun, 03 Jun 2012 12:09:41 +0400
parents	a3e439d09322
children	bc1a7595d9d1

line source

1 """Miscellanous utilities.

2 """

3 import sys

4 import warnings

5 import os

6 from tempfile import mkstemp

7 from StringIO import StringIO

9 def unzip(seq):

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

11 a, b = [], []

12 for x, y in seq:

13 a.append(x)

14 b.append(y)

15 return a, b

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

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

19 if filename == '-':

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

21 return sys.stdout

22 if 'r' in mode:

23 return sys.stdin

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

25 else:

26 return file(filename, mode)

28 def remove_each(string, substrings):

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

30 for sub in substrings:

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

32 return string

34 class UserDict(dict):

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

36 pass

38 class UserList(list):

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

40 pass

42 class UserString(str):

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

44 pass

46 def deprecated(message):

47 """Warn about function being deprecated."""

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

50 class Silence(object):

51 """Context manager for use with `with`.

53 Run code in context without any message to the screen, but show all output

54 that was there if an error occured. E.g.::

56 with Silence():

57 structure = PDBParser().get_structure(name, file)

59 There are two mutually exclusive ways of silencing:

61 1. By replacing OS'es stdout/stderr with tempfile (called `dup`)

62 2. By replacing python's sys.stdout/sys.stderr with StringIO (`hide`)

64 For each of ways you may specify values: 'stdout', 'stderr' or 'both'.

65 E.g::

67 with Silence(dup="both"):

68 check_call(["mucle", alignment])

70 `Silence()` is equivalent to `Silence(hide='stderr')`

71 """

73 def __init__(self, hide=None, dup=None):

74 if dup is None and hide is None:

75 hide = "stderr"

76 assert not (dup is not None and hide is not None)

77 self.stderr = self.stdout = self.dup_stderr = self.dup_stdout = False

78 if dup == "stdout" or dup == "both":

79 self.dup_stdout = True

80 if dup == "stderr" or dup == "both":

81 self.dup_stderr = True

82 if hide == "stdout" or hide == "both":

83 self.stdout = True

84 if hide == "stderr" or hide == "both":

85 self.stderr = True

87 def __enter__(self):

88 assert not (self.stderr and self.dup_stderr)

89 assert not (self.stdout and self.dup_stdout)

90 if self.dup_stdout or self.dup_stderr:

91 fd, name = mkstemp(prefix="allpy-silent-")

92 self.captured_dup = os.fdopen(fd)

93 self.captured_dup_name = name

94 if self.dup_stdout:

95 self.dup_stdout = os.dup(sys.stdout.fileno())

96 os.dup2(self.captured_dup.fileno(), sys.stdout.fileno())

97 if self.dup_stderr:

98 self.dup_stderr = os.dup(sys.stderr.fileno())

99 os.dup2(self.captured_dup.fileno(), sys.stderr.fileno())

100 if self.stdout or self.stderr:

101 self.captured_output = StringIO()

102 if self.stdout:

103 self.stdout, sys.stdout = sys.stdout, self.captured_output

104 if self.stderr:

105 self.stderr, sys.stderr = sys.stderr, self.captured_output

106

107 def __exit__(self, exc_type, exc_value, traceback):

108 if self.stdout or self.stderr:

109 if self.stdout:

110 sys.stdout = self.stdout

111 if self.stderr:

112 sys.stderr = self.stderr

113 if exc_type is not None:

114 sys.stderr.write(self.captured_output.getvalue())

115 if self.dup_stdout or self.dup_stderr:

116 if self.dup_stdout:

117 os.dup2(self.dup_stdout, sys.stdout.fileno())

118 os.close(self.dup_stdout)

119 if self.dup_stderr:

120 os.dup2(self.dup_stderr, sys.stderr.fileno())

121 os.close(self.dup_stderr)

122 if exc_type is not None:

123 self.captured_dup.seek(0)

124 sys.stderr.write(self.captured_dup.read())

125 os.unlink(self.captured_dup_name)

126

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