allpy: lib/block.py annotate

allpy

annotate lib/block.py @ 124:9f96bc38bc3d

broken: lib::block::geometrical_core retirns block, not position list

author	boris <bnagaev@gmail.com>
date	Sat, 23 Oct 2010 23:32:52 +0400
parents	b7c3691c47bf
children	c84a7840f9b8

rev	line source
BurkovBA@0	1 #!usr/bin/python
BurkovBA@0	2
BurkovBA@0	3 import sys
BurkovBA@0	4
BurkovBA@0	5 import project
BurkovBA@0	6 import sequence
BurkovBA@0	7 import monomer
bnagaev@116	8 import config
bnagaev@121	9 from graph import Graph
bnagaev@124	10 from copy import copy
BurkovBA@0	11
BurkovBA@0	12 class Block(object):
BurkovBA@0	13 """
BurkovBA@0	14 Mandatory data:
BurkovBA@0	15 * self.project -- project object, which the block belongs to
BurkovBA@1	16 * self.sequences - set of sequence objects that contain monomers
BurkovBA@0	17 and/or gaps, that constitute the block
bnagaev@115	18 * self.positions -- sorted list of positions of the project.alignment that
BurkovBA@1	19 are included in the block
bnagaev@116	20
BurkovBA@0	21 How to create a new block:
BurkovBA@0	22 >>> import project
BurkovBA@0	23 >>> import block
BurkovBA@0	24 >>> proj = project.Project(open("test.fasta"))
bnagaev@114	25 >>> block1 = block.Block(proj)
BurkovBA@0	26 """
BurkovBA@0	27
bnagaev@112	28 def __init__(self, project, sequences=None, positions=None):
bnagaev@112	29 """
bnagaev@112	30 Builds new block from project
bnagaev@112	31 if sequences==None, all sequences are used
bnagaev@112	32 if positions==None, all positions are used
bnagaev@112	33 """
bnagaev@112	34 if sequences == None:
bnagaev@112	35 sequences = project.sequences
bnagaev@112	36 if positions == None:
bnagaev@112	37 positions = range(len(project))
BurkovBA@73	38 self.project = project
BurkovBA@73	39 self.sequences = sequences
BurkovBA@73	40 self.positions = positions
BurkovBA@0	41
bnagaev@112	42 def save_fasta(self, out_file, long_line=60):
bnagaev@112	43 """
bnagaev@112	44 Saves alignment to given file in fasta-format
bnagaev@112	45 Splits long lines to substrings of length=long_line
bnagaev@112	46 To prevent this, set long_line=None
bnagaev@112	47
BurkovBA@0	48 No changes in the names, descriptions or order of the sequences
BurkovBA@0	49 are made.
BurkovBA@0	50 """
BurkovBA@0	51 for sequence in self.sequences:
bnagaev@112	52 out_file.write(">%(name)s %(description)s \n" % sequence.__dict__)
bnagaev@113	53 alignment_monomers = self.project.alignment[sequence]
bnagaev@115	54 block_monomers = [alignment_monomers[i] for i in self.positions]
bnagaev@113	55 string = ''.join([m.type.code1 if m else '-' for m in block_monomers])
bnagaev@112	56 if long_line:
bnagaev@112	57 for i in range(0, len(string) // long_line + 1):
bnagaev@112	58 out_file.write("%s \n" % string[ilong_line : ilong_line + long_line])
bnagaev@112	59 else:
bnagaev@112	60 out_file.write("%s \n" % string)
bnagaev@116	61
bnagaev@120	62 def geometrical_core(self, max_delta=config.delta,
bnagaev@120	63 timeout=config.timeout, minsize=config.minsize):
bnagaev@116	64 """
bnagaev@124	65 returns new block, representing geometrical core
bnagaev@124	66
bnagaev@116	67 delta -- threshold of distance spreading
bnagaev@120	68
bnagaev@120	69 If more than one pdb chain for some sequence provided, consider all of them
bnagaev@120	70 cost is calculated as 1 / (delta + 1)
bnagaev@120	71 delta in [0, +inf) => cost in (0, 1]
bnagaev@116	72 """
bnagaev@117	73 nodes = self.positions
bnagaev@117	74 lines = {}
bnagaev@116	75 for i in self.positions:
bnagaev@116	76 for j in self.positions:
bnagaev@117	77 if i < j:
bnagaev@120	78 distances = []
bnagaev@120	79 for sequence in self.sequences:
bnagaev@120	80 for chain in sequence.pdb_chains:
bnagaev@120	81 m1 = self.project.alignment[sequence][i]
bnagaev@120	82 m2 = self.project.alignment[sequence][j]
bnagaev@122	83 if m1 and m2:
bnagaev@122	84 ca1 = m1.pdb_residues[chain]['CA']
bnagaev@122	85 ca2 = m2.pdb_residues[chain]['CA']
bnagaev@122	86 d = ca1 - ca2 # Bio.PDB feature
bnagaev@122	87 distances.append(d)
bnagaev@122	88 if len(distances) >= 2:
bnagaev@122	89 delta = max(distances) - min(distances)
bnagaev@122	90 if delta <= max_delta:
bnagaev@122	91 lines[Graph.line(i, j)] = 1.0 / (1.0 + max_delta)
bnagaev@120	92 graph = Graph(nodes, lines)
bnagaev@124	93 positions = graph.cliques(timeout=timeout, minsize=minsize)
bnagaev@124	94 return Block(self.project, copy(self.sequences), positions)
bnagaev@123	95
bnagaev@123	96 def xstring(self, x):
bnagaev@123	97 """
bnagaev@123	98 Returns string consisting of '-' and chars x at self.positions
bnagaev@123	99 Length of returning string = length of project
bnagaev@123	100 """
bnagaev@123	101 monomers = [False] * len(self.project)
bnagaev@123	102 for i in self.positions:
bnagaev@123	103 monomers[i] = True
bnagaev@123	104 return ''.join([x if m else '-' for m in monomers])