class Bio::Sim4

The sim4 execution wrapper class.

Attributes

command[R]

last command-line strings executed by the object

database[RW]

default file name of database(‘seq2’)

options[RW]

options

output[R]

last result text (String)

program[R]

name of the program (usually ‘sim4’ in UNIX)

report[R]

last result. Returns a Bio::Sim4::Report object.

Public Class Methods

new(program = 'sim4', database = nil, opt = []) click to toggle source

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).

   # File lib/bio/appl/sim4.rb
32 def initialize(program = 'sim4', database = nil, opt = [])
33   @program = program
34   @options = opt
35   @database = database #seq2
36   @command = nil
37   @output = nil
38   @report = nil
39 end

Public Instance Methods

exec(filename1, filename2 = nil)

Alias for: exec_local

exec_local(filename1, filename2 = nil) click to toggle source

Executes the sim4 program. Perform mRNA-genome alignment between sequences in given files. filename1 and filename2 should be file name strings. If filename2 is not specified, using self.database.

    # File lib/bio/appl/sim4.rb
109 def exec_local(filename1, filename2 = nil)
110   @command = [ @program, filename1, (filename2 or @database), *@options ]
111   @output = nil
112   @report = nil
113   Bio::Command.call_command(@command) do |io|
114     io.close_write
115     @output = io.read
116     @report = Bio::Sim4::Report.new(@output)
117   end
118   @report
119 end

Also aliased as: exec

log() click to toggle source

log is deprecated (no replacement) and returns empty string.

   # File lib/bio/appl/sim4.rb
65 def log
66   warn "log is deprecated (no replacement) and returns empty string."
67   ''
68 end

option() click to toggle source

option is deprecated. Instead, please use options.

   # File lib/bio/appl/sim4.rb
51 def option
52   warn "option is deprecated. Please use options."
53   options
54 end

query(seq1) click to toggle source

Executes the sim4 program. seq1 shall be a Bio::Sequence object. Returns a Bio::Sim4::Report object.

   # File lib/bio/appl/sim4.rb
79 def query(seq1)
80   tf = Tempfile.open('sim4')
81   tf.print seq1.to_fasta('seq1', 70)
82   tf.close(false)
83   r = exec_local(tf.path)
84   tf.close(true)
85   r
86 end

query_pairwise(seq1, seq2) click to toggle source

Executes the sim4 program. Perform mRNA-genome alignment between given sequences. seq1 and seq2 should be Bio::Sequence objects. Returns a Bio::Sim4::Report object.

    # File lib/bio/appl/sim4.rb
 92 def query_pairwise(seq1, seq2)
 93   tf = Tempfile.open('sim4')
 94   tf.print seq1.to_fasta('seq1', 70)
 95   tf.close(false)
 96   tf2 = Tempfile.open('seq2')
 97   tf2.print seq1.to_fasta('seq2', 70)
 98   tf2.close(false)
 99   r = exec_local(tf.path, tf2.path)
100   tf.close(true)
101   tf2.close(true)
102   r
103 end