1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
|
#
# = bio/appl/sim4.rb - sim4 wrapper class
#
# Copyright:: Copyright (C) 2004 GOTO Naohisa <ng@bioruby.org>
# License:: The Ruby License
#
# $Id: sim4.rb,v 1.10 2007/04/05 23:35:39 trevor Exp $
#
# The sim4 execution wrapper class.
#
# == References
#
# * Florea, L., et al., A Computer program for aligning a cDNA sequence
# with a genomic DNA sequence, Genome Research, 8, 967--974, 1998.
# http://www.genome.org/cgi/content/abstract/8/9/967
#
require 'tempfile'
require 'bio/command'
module Bio
# The sim4 execution wrapper class.
class Sim4
autoload :Report, 'bio/appl/sim4/report'
# Creates a new sim4 execution wrapper object.
# [+program+] Program name. Usually 'sim4' in UNIX.
# [+database+] Default file name of database('seq2').
# [+option+] Options (array of strings).
def initialize(program = 'sim4', database = nil, opt = [])
@program = program
@options = opt
@database = database #seq2
@command = nil
@output = nil
@report = nil
end
# default file name of database('seq2')
attr_accessor :database
# name of the program (usually 'sim4' in UNIX)
attr_reader :program
# options
attr_accessor :options
# option is deprecated. Instead, please use options.
def option
warn "option is deprecated. Please use options."
options
end
# last command-line strings executed by the object
attr_reader :command
#---
# last messages of program reported to the STDERR
#attr_reader :log
#+++
#log is deprecated (no replacement) and returns empty string.
def log
warn "log is deprecated (no replacement) and returns empty string."
''
end
# last result text (String)
attr_reader :output
# last result. Returns a Bio::Sim4::Report object.
attr_reader :report
# Executes the sim4 program.
# <tt>seq1</tt> shall be a Bio::Sequence object.
# Returns a Bio::Sim4::Report object.
def query(seq1)
tf = Tempfile.open('sim4')
tf.print seq1.to_fasta('seq1', 70)
tf.close(false)
r = exec_local(tf.path)
tf.close(true)
r
end
# Executes the sim4 program.
# Perform mRNA-genome alignment between given sequences.
# <tt>seq1</tt> and <tt>seq2</tt> should be Bio::Sequence objects.
# Returns a Bio::Sim4::Report object.
def query_pairwise(seq1, seq2)
tf = Tempfile.open('sim4')
tf.print seq1.to_fasta('seq1', 70)
tf.close(false)
tf2 = Tempfile.open('seq2')
tf2.print seq1.to_fasta('seq2', 70)
tf2.close(false)
r = exec_local(tf.path, tf2.path)
tf.close(true)
tf2.close(true)
r
end
# Executes the sim4 program.
# Perform mRNA-genome alignment between sequences in given files.
# <tt>filename1</tt> and <tt>filename2</tt> should be file name strings.
# If <tt>filename2</tt> is not specified, using <tt>self.database</tt>.
def exec_local(filename1, filename2 = nil)
@command = [ @program, filename1, (filename2 or @database), *@options ]
@output = nil
@report = nil
Bio::Command.call_command(@command) do |io|
io.close_write
@output = io.read
@report = Bio::Sim4::Report.new(@output)
end
@report
end
alias exec exec_local
end #class Sim4
end #module Bio
|
