allpy: 21cfc7897a8f allpy/markups.py

allpy

view allpy/markups.py @ 711:21cfc7897a8f

Implemented markup fileIO (closes #56) This is done by adding file format 'markup' or 'markup:formatname', where 'formatname' is otherwise known alignment format. The file format for is described briefly in fileio.MarkupFile docstrings. This commit also contains example of defining Markup saving mixin: markups.IntMarkupMixin and a test for it.

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Thu, 07 Jul 2011 22:32:21 +0400
parents	df624c729ab5
children	52ce523138d5

line source

1 import base

3 class IntMarkupMixin(base.Markup):

5 @classmethod

6 def from_record(cls, container, record, name=None):

7 assert record['io-class'] == 'IntMarkup'

8 result = cls(container, name=name)

9 separator = record.get('separator', ',')

10 values = record['markup'].split(separator)

11 assert len(values) == len(result.sorted_keys())

12 for key, value in zip(result.sorted_keys(), values):

13 if value:

14 result[key] = int(value)

15 return result

17 def to_record(self):

18 def fmt(value):

19 if value is None:

20 return ""

21 return str(value)

22 values = [fmt(self.get(key)) for key in self.sorted_keys()]

23 return {'markup': ','.join(values), 'io-class': 'IntMarkup'}

25 class SequenceNumberMarkup(base.SequenceMarkup):

27 name = 'number'

29 def refresh(self):

30 for number, monomer in enumerate(self.sequence, 1):

31 monomer.number = number

33 class SequenceIndexMarkup(base.SequenceMarkup):

35 name = 'index'

37 def refresh(self):

38 for index, monomer in enumerate(self.sequence):

39 monomer.index = index

41 class AlignmentNumberMarkup(base.AlignmentMarkup):

43 name = 'number'

45 def refresh(self):

46 for number, column in enumerate(self.alignment.columns, 1):

47 self[column] = number

49 class AlignmentIndexMarkup(base.AlignmentMarkup):

51 name = 'index'

53 def refresh(self):

54 for index, column in enumerate(self.alignment.columns):

55 self[column] = index

57 class SequenceCaseMarkup(base.SequenceMarkup):

59 name = 'case'

61 def refresh(self):

62 for monomer in self.sequence:

63 if monomer.input_code1.isupper():

64 monomer.case = 'upper'

65 elif monomer.input_code1.islower():

66 monomer.case = 'lower'

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