allpy: lib/block.py annotate

allpy

annotate lib/block.py @ 112:b7b963287d31

broken: lib::block::to_fasta -> save_fasta

author	boris <bnagaev@gmail.com>
date	Sat, 23 Oct 2010 13:16:12 +0400
parents	217d83a617c3
children	90e2c77b69b7

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
BurkovBA@0	8
BurkovBA@0	9 class Block(object):
BurkovBA@0	10 """
BurkovBA@0	11 Mandatory data:
BurkovBA@0	12 * self.project -- project object, which the block belongs to
BurkovBA@1	13 * self.sequences - set of sequence objects that contain monomers
BurkovBA@0	14 and/or gaps, that constitute the block
BurkovBA@1	15 * self.positions -- list of positions of the project.alignment that
BurkovBA@1	16 are included in the block
BurkovBA@0	17
BurkovBA@0	18 How to create a new block:
BurkovBA@0	19 >>> import project
BurkovBA@0	20 >>> import block
BurkovBA@0	21 >>> proj = project.Project(open("test.fasta"))
BurkovBA@0	22 >>> block1 = block.Block(proj, proj.sequences, range(len(proj.alignment[proj.sequences[0]])))
BurkovBA@0	23
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@112	51 monomers = [self.project.alignment[i] for i in sorted(self.positions)]
bnagaev@112	52 string = ''.join([m.type.code1 if m else '-' for m in monomers])
bnagaev@112	53 if long_line:
bnagaev@112	54 for i in range(0, len(string) // long_line + 1):
bnagaev@112	55 out_file.write("%s \n" % string[ilong_line : ilong_line + long_line])
bnagaev@112	56 else:
bnagaev@112	57 out_file.write("%s \n" % string)