allpy: 6190c12fcb45 allpy/markups.py

allpy

Makes (case sensitive by request) homology classes for a number of input fasta alignments

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: