allpy: df571a5233fb allpy/protein.py

allpy

view allpy/protein.py @ 382:df571a5233fb

Changed the way related types are stored for Alignment, Block, Sequence, Monomer Now each of them has attribute 'type', which is an object with four attributes: - Alignment - Block - Sequence - Monomer

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Tue, 01 Feb 2011 23:08:08 +0300
parents	5639138f619a
children	01f9e9c3493e

line source

1 import base

2 import data.codes

4 import protein

6 class Monomer(base.Monomer):

7 """Protein monomers: aminoacids."""

8 type = 'protein'

9 types = protein

10 by_code1 = {}

11 by_code3 = {}

12 by_name = {}

13 Monomer._initialize(data.codes.protein)

15 class Protein(list):

16 """User defined protein; list of protein_sequences."""

17 pass

19 class Sequence(base.Sequence):

20 types = protein

22 class Block(Alignment, base.Block):

23 pass

25 class Alignment(base.Alignment):

26 types = protein

28 def muscle_align(self):

29 """ Simple align ths alignment using sequences (muscle)

31 uses old Monomers and Sequences objects

32 """

33 tmp_file = NamedTemporaryFile(delete=False)

34 self.save_fasta(tmp_file)

35 tmp_file.close()

36 os.system("muscle -in %(tmp)s -out %(tmp)s" % {'tmp': tmp_file.name})

37 sequences, body = Alignment.from_file(open(tmp_file.name))

38 for sequence in self.sequences:

39 try:

40 new_sequence = [i for i in sequences if sequence==i][0]

41 except:

42 raise Exception("Align: Cann't find sequence %s in muscle output" % \

43 sequence.name)

44 old_monomers = iter(sequence.monomers)

45 self.body[sequence] = []

46 for monomer in body[new_sequence]:

47 if not monomer:

48 self.body[sequence].append(monomer)

49 else:

50 old_monomer = old_monomers.next()

51 if monomer != old_monomer:

52 raise Exception("Align: alignment errors")

53 self.body[sequence].append(old_monomer)

54 os.unlink(tmp_file.name)

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