allpy: lib/block.py annotate

allpy

annotate lib/block.py @ 120:5e7851709c95

lib::block geometrical_core completed, not tested

author	boris <bnagaev@gmail.com>
date	Sat, 23 Oct 2010 22:45:35 +0400
parents	fd7371f14c6d
children	0903179f8c34

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