Class: Bio::Sim4

Inherits:
Object show all
Defined in:
lib/bio/appl/sim4.rb,
lib/bio/appl/sim4/report.rb

Overview

The sim4 execution wrapper class.

Defined Under Namespace

Classes: Report

Instance Attribute Summary (collapse)

Instance Method Summary (collapse)

Constructor Details

- (Sim4) initialize(program = 'sim4', database = nil, opt = [])

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).



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# File 'lib/bio/appl/sim4.rb', line 32

def initialize(program = 'sim4', database = nil, opt = [])
  @program = program
  @options = opt
  @database = database #seq2
  @command = nil
  @output = nil
  @report = nil
end

Instance Attribute Details

- (Object) command (readonly)

last command-line strings executed by the object



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# File 'lib/bio/appl/sim4.rb', line 57

def command
  @command
end

- (Object) database

default file name of database('seq2')



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# File 'lib/bio/appl/sim4.rb', line 42

def database
  @database
end

- (Object) options

options



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# File 'lib/bio/appl/sim4.rb', line 48

def options
  @options
end

- (Object) output (readonly)

last result text (String)



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# File 'lib/bio/appl/sim4.rb', line 71

def output
  @output
end

- (Object) program (readonly)

name of the program (usually 'sim4' in UNIX)



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# File 'lib/bio/appl/sim4.rb', line 45

def program
  @program
end

- (Object) report (readonly)

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



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# File 'lib/bio/appl/sim4.rb', line 74

def report
  @report
end

Instance Method Details

- (Object) exec_local(filename1, filename2 = nil) Also known as: exec

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.



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# File 'lib/bio/appl/sim4.rb', line 109

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

- (Object) log

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



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# File 'lib/bio/appl/sim4.rb', line 65

def log
  warn "log is deprecated (no replacement) and returns empty string."
  ''
end

- (Object) option

option is deprecated. Instead, please use options.



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# File 'lib/bio/appl/sim4.rb', line 51

def option
  warn "option is deprecated. Please use options."
  options
end

- (Object) query(seq1)

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



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# File 'lib/bio/appl/sim4.rb', line 79

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

- (Object) query_pairwise(seq1, seq2)

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.



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# File 'lib/bio/appl/sim4.rb', line 92

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