allpy
view allpy/markup.py @ 973:325d165af197
allpy.processors: use NamedTemporaryFile(..., delete=True) in favour of removing the files manually (closes #137)
While writing the relevant line I failed to read the docs properly and was under impression that delete=True refers to the hack, when one creates the file and removes it at once before writing any data to it for the sake of making the file invisible. Which is actually not the case, and the file is removed after being closed.
author | Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru> |
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date | Sat, 25 Feb 2012 20:16:51 +0400 |
parents | 3566d253c994 |
children |
line source
4 """ object for use as key for default value """
7 """ Markup for Sequence or Alignment
9 container is iterable collection of items.
10 item is object getting markup data (new attribute).
12 container: Alignment, item: Column
13 container: Sequence, item: Monomer
15 Markup stored in attributes of item is internal value.
16 When export or import, it is mapped to or from external value.
17 Internal value could be of any type.
18 External value should be single character.
20 Data:
21 * name -- name (str) of attribute of object
22 * container
23 * map_out -- dict, mapping internal values to external
24 * map_in -- dict, mapping external values to internal
26 map_in and map_out can have key markup.default, which used when
27 input key is not in map. To drop this defaults, drop this key
28 from map_out and map_in dicts. In this case to_string() and
29 from_string() methods can raise KeyError
30 """
33 """ Note: add convenient defaults to maps """
55 """ return internal value for given item
57 markup[monomer] <==> monomer.name, where name is markup.name
58 """
62 """ set attribute of item to value """
66 """ return item has attribute
68 usage: if item in markup
69 """
73 """ delete all attributes from items """
78 """ return string representing markup """
87 @classmethod
89 """ return new markup
91 add (or replaces) attributes to items
92 """
104 """ return list of tuples (item, self[item]) for items with attribute """
110 """ return list of items for with attribute is determined """