allpy: 505ce122068b lib/block.py

allpy

Generalized tcl examples in the sandbox.

author	Danya Alexeyevsky <me.dendik@gmail.com>
date	Thu, 10 Jun 2010 14:24:08 +0400
parents	757f2a1f8732
children	217d83a617c3

line source

1 #!usr/bin/python

3 import sys

5 import project

6 import sequence

7 import monomer

9 class Block(object):

10 """

11 Mandatory data:

12 * self.project -- project object, which the block belongs to

13 * self.sequences - set of sequence objects that contain monomers

14 and/or gaps, that constitute the block

15 * self.positions -- list of positions of the project.alignment that

16 are included in the block

18 How to create a new block:

19 >>> import project

20 >>> import block

21 >>> proj = project.Project(open("test.fasta"))

22 >>> block1 = block.Block(proj, proj.sequences, range(len(proj.alignment[proj.sequences[0]])))

24 """

26 def __init__(self,project,sequences,positions):

27 self.project=project

28 self.sequences=sequences

29 self.positions=positions

31 def to_fasta(self,file):

32 """writes the block as an alignment in fasta-format into the file.

34 No changes in the names, descriptions or order of the sequences

35 are made.

37 """

38 for sequence in self.sequences:

39 file.write(">%s %s\n"%(sequence.name,sequence.description))

40 string_index=0

41 for position in self.positions:

42 if string_index>=60:

43 file.write("\n")

44 string_index=0

45 if self.project.alignment[sequence][position]==None:

46 file.write("-")

47 string_index+=1

48 else:

49 file.write(self.project.alignment[sequence][position].code)

50 string_index+=1

51 file.write("\n")