allpy: 166806efc570 allpy/protein.py

allpy

view allpy/protein.py @ 373:166806efc570

base.Alignment.process: added parameters to control what to copy also, cleaned up code

author	Daniil Alexeyevsky <me.dendik@gmail.com>
date	Mon, 31 Jan 2011 19:12:05 +0300
parents	0411fa851bba
children	5639138f619a

line source

1 import base

2 import data.codes

4 class Monomer(base.Monomer):

5 """Protein monomers: aminoacids."""

6 type = 'protein'

7 by_code1 = {}

8 by_code3 = {}

9 by_name = {}

10 Monomer._initialize(data.codes.protein)

12 class Protein(list):

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

14 pass

16 class Sequence(base.Sequence):

17 monomer_type = Monomer

19 class Alignment(base.Alignment):

20 sequence_type = Sequence

22 def muscle_align(self):

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

25 uses old Monomers and Sequences objects

26 """

27 tmp_file = NamedTemporaryFile(delete=False)

28 self.save_fasta(tmp_file)

29 tmp_file.close()

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

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

32 for sequence in self.sequences:

33 try:

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

35 except:

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

37 sequence.name)

38 old_monomers = iter(sequence.monomers)

39 self.body[sequence] = []

40 for monomer in body[new_sequence]:

41 if not monomer:

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

43 else:

44 old_monomer = old_monomers.next()

45 if monomer != old_monomer:

46 raise Exception("Align: alignment errors")

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

48 os.unlink(tmp_file.name)

50 class Block(Alignment, base.Block):

51 pass

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