allpy: 696d314ad718 allpy/protein.py

allpy

view allpy/protein.py @ 322:696d314ad718

Added to base.Monomer missing properties: code1, code3, name, is_modified

author	Daniil Alexeyevsky <me.dendik@gmail.com>
date	Fri, 17 Dec 2010 00:35:31 +0300
parents	be9c3cacd009
children	e3bcb9f8d7b0

line source

1 import base

3 class MonomerType(base.MonomerType):

4 by_code1 = {}

5 by_code3 = {}

6 by_name = {}

8 class Monomer(base.Monomer):

9 """Protein monomers: aminoacids."""

10 monomer_type = MonomerType

12 MonomerType._initialize('p')

13 MonomerType.instance_type = Monomer

15 class Protein(list):

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

17 pass

19 class Sequence(base.Sequence):

20 monomer_type = Monomer

22 class Alignment(base.Alignment):

23 sequence_type = Sequence

25 def muscle_align(self):

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

28 uses old Monomers and Sequences objects

29 """

30 tmp_file = NamedTemporaryFile(delete=False)

31 self.save_fasta(tmp_file)

32 tmp_file.close()

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

34 sequences, body = Alignment.from_fasta(open(tmp_file.name))

35 for sequence in self.sequences:

36 try:

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

38 except:

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

40 sequence.name)

41 old_monomers = iter(sequence.monomers)

42 self.body[sequence] = []

43 for monomer in body[new_sequence]:

44 if not monomer:

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

46 else:

47 old_monomer = old_monomers.next()

48 if monomer != old_monomer:

49 raise Exception("Align: alignment errors")

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

51 os.unlink(tmp_file.name)

53 class Block(Alignment, base.Block):

54 pass

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