allpy: 80043822a41e allpy/markups.py

allpy

view allpy/markups.py @ 704:80043822a41e

Added fileio.File.read_alignment and fileio.File.write_alignment [closes #57] This is now the recommended interface. In the following commits this interface will be used to write markup together with alignment. Previously, fileio received the alignment torn-apart into sequence representations as strings with gaps, sequence names and descriptions. Now, fileio tears the alignment apart by itself.

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Thu, 07 Jul 2011 19:21:12 +0400
parents	4d1f5ece3f0a
children	21cfc7897a8f

line source

1 import base

3 class SequenceNumberMarkup(base.SequenceMarkup):

5 name = 'number'

7 def refresh(self):

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

9 monomer.number = number

11 class SequenceIndexMarkup(base.SequenceMarkup):

13 name = 'index'

15 def refresh(self):

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

17 monomer.index = index

19 class AlignmentNumberMarkup(base.AlignmentMarkup):

21 name = 'number'

23 def refresh(self):

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

25 self[column] = number

27 class AlignmentIndexMarkup(base.AlignmentMarkup):

29 name = 'index'

31 def refresh(self):

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

33 self[column] = index

35 class SequenceCaseMarkup(base.SequenceMarkup):

37 name = 'case'

39 def refresh(self):

40 for monomer in self.sequence:

41 if monomer.input_code1.isupper():

42 monomer.case = 'upper'

43 elif monomer.input_code1.islower():

44 monomer.case = 'lower'

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