class Bio::HMMER
Description¶ ↑
A wapper for HMMER programs (hmmsearch or hmmpfam).
Examples¶ ↑
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
References¶ ↑
Attributes
Name of hmmfile.
Command line options.
Shows the raw output from the hmmer search.
Prgrams name. (hmmsearch or hmmpfam).
Name of seqfile.
Public Class Methods
Source
# File lib/bio/appl/hmmer.rb 60 def initialize(program, hmmfile, seqfile, options = []) 61 @program = program 62 @hmmfile = hmmfile 63 @seqfile = seqfile 64 @output = '' 65 66 begin 67 @options = options.to_ary 68 rescue NameError #NoMethodError 69 # backward compatibility 70 @options = Shellwords.shellwords(options) 71 end 72 end
Sets a program name, a profile hmm file name, a query sequence file name and options in string.
Program names: hmmsearch, hmmpfam
Source
# File lib/bio/appl/hmmer/report.rb 62 def self.reports(multiple_report_text) 63 ary = [] 64 multiple_report_text.each_line("\n//\n") do |report| 65 if block_given? 66 yield Report.new(report) 67 else 68 ary << Report.new(report) 69 end 70 end 71 return ary 72 end
A reader interface for multiple reports text into a report (Bio::HMMER::Report).
Examples¶ ↑
# Iterator Bio::HMMER.reports(reports_text) do |report| report end # Array reports = Bio::HMMER.reports(reports_text)
Public Instance Methods
Source
# File lib/bio/appl/hmmer.rb 77 def option 78 Bio::Command.make_command_line(@options) 79 end
Gets options by String. backward compatibility.
Source
# File lib/bio/appl/hmmer.rb 84 def option=(str) 85 @options = Shellwords.shellwords(str) 86 end
Sets options by String. backward compatibility.
Source
# File lib/bio/appl/hmmer.rb 91 def query 92 cmd = [ @program, *@options ] 93 cmd.concat([ @hmmfile, @seqfile ]) 94 95 report = nil 96 97 @output = Bio::Command.query_command(cmd, nil) 98 report = parse_result(@output) 99 100 return report 101 end
Executes the hmmer search and returns the report (Bio::HMMER::Report object).