Class: Bio::HMMER

Inherits:

Object

• Object
• Bio::HMMER

show all

Defined in:

lib/bio/appl/hmmer.rb,
lib/bio/appl/hmmer/report.rb

Overview

require 'bio'
program = 'hmmsearch' # or 'hmmpfam'
hmmfile = 'test.hmm'
seqfile = 'test.faa'

factory = Bio::HMMER.new(program, hmmfile, seqfile)
report = factory.query
report.class # => Bio::HMMER::Report

Defined Under Namespace

Classes: Report

Instance Attribute Summary (collapse)

• - (Object) hmmfile

  Name of hmmfile.

• - (Object) options

  Command line options.

• - (Object) output readonly

  Shows the raw output from the hmmer search.

• - (Object) program

  Prgrams name.

• - (Object) seqfile

  Name of seqfile.

Class Method Summary (collapse)

• + (Object) reports(multiple_report_text)

  A reader interface for multiple reports text into a report (Bio::HMMER::Report).

Instance Method Summary (collapse)

• - (HMMER) initialize(program, hmmfile, seqfile, options = []) constructor

  Sets a program name, a profile hmm file name, a query sequence file name and options in string.

• - (Object) option

  Gets options by String.

• - (Object) option=(str)

  Sets options by String.

• - (Object) query

  Executes the hmmer search and returns the report (Bio::HMMER::Report object).

60
61
62
63
64
65
66
67
68
69
70
71
72

# File 'lib/bio/appl/hmmer.rb', line 60

def initialize(program, hmmfile, seqfile, options = [])
  @program = program
  @hmmfile = hmmfile
  @seqfile = seqfile
  @output  = ''
  
  begin
    @options = options.to_ary
  rescue NameError #NoMethodError
    # backward compatibility
    @options = Shellwords.shellwords(options)
  end
end

44
45
46

# File 'lib/bio/appl/hmmer.rb', line 44

def hmmfile
  @hmmfile
end

50
51
52

# File 'lib/bio/appl/hmmer.rb', line 50

def options
  @options
end

53
54
55

# File 'lib/bio/appl/hmmer.rb', line 53

def output
  @output
end

41
42
43

# File 'lib/bio/appl/hmmer.rb', line 41

def program
  @program
end

47
48
49

# File 'lib/bio/appl/hmmer.rb', line 47

def seqfile
  @seqfile
end

# Iterator
Bio::HMMER.reports(reports_text) do |report|
  report
end

# Array
reports = Bio::HMMER.reports(reports_text)

62
63
64
65
66
67
68
69
70
71
72

# File 'lib/bio/appl/hmmer/report.rb', line 62

def self.reports(multiple_report_text)
  ary = []
  multiple_report_text.each_line("\n//\n") do |report|
    if block_given?
      yield Report.new(report)
    else
      ary << Report.new(report)
    end
  end
  return ary
end

77
78
79

# File 'lib/bio/appl/hmmer.rb', line 77

def option
  Bio::Command.make_command_line(@options)
end

84
85
86

# File 'lib/bio/appl/hmmer.rb', line 84

def option=(str)
  @options = Shellwords.shellwords(str)
end

91
92
93
94
95
96
97
98
99
100
101

# File 'lib/bio/appl/hmmer.rb', line 91

def query
  cmd = [ @program, *@options ]
  cmd.concat([ @hmmfile, @seqfile ])
    
  report = nil
  
  @output = Bio::Command.query_command(cmd, nil)
  report = parse_result(@output)
    
  return report
end