Class: Genfrag::App
- Inherits:
-
Object
- Object
- Genfrag::App
- Defined in:
- lib/genfrag/app.rb,
lib/genfrag/app/command.rb,
lib/genfrag/app/index_command.rb,
lib/genfrag/app/search_command.rb,
lib/genfrag/app/index_command/db.rb,
lib/genfrag/app/search_command/trim.rb,
lib/genfrag/app/search_command/match.rb,
lib/genfrag/app/search_command/process_file.rb
Defined Under Namespace
Classes: Command, IndexCommand, SearchCommand
Class Method Summary collapse
-
.cli_run(args) ⇒ Object
Create a new instance of App, and run the
genfrag
application given the command line args.
Instance Method Summary collapse
-
#cli_run(args) ⇒ Object
Parse the desired user command and run that command object.
-
#help ⇒ Object
Show the toplevel help message.
-
#initialize(out = STDOUT, err = STDERR) ⇒ App
constructor
Create a new main instance using io for standard output and err for error messages.
Constructor Details
#initialize(out = STDOUT, err = STDERR) ⇒ App
Create a new main instance using io for standard output and err for error messages.
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# File 'lib/genfrag/app.rb', line 30 def initialize( out = STDOUT, err = STDERR ) @out = out @err = err end |
Class Method Details
.cli_run(args) ⇒ Object
Create a new instance of App, and run the genfrag
application given the command line args.
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# File 'lib/genfrag/app.rb', line 23 def self.cli_run( args ) self.new.cli_run args end |
Instance Method Details
#cli_run(args) ⇒ Object
Parse the desired user command and run that command object.
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# File 'lib/genfrag/app.rb', line 37 def cli_run( args ) cmd_str = args.shift cmd = case cmd_str when 'index'; IndexCommand.new(@out, @err) when 'search'; SearchCommand.new(@out, @err) when 'info'; InfoCommand.new(@out, @err) when nil, '-h', '--help' help when '-V', '--version' @out.puts "Genfrag #{::Genfrag::VERSION}" nil else @err.puts "Unknown command #{cmd_str.inspect}" help nil end cmd.cli_run args if cmd rescue StandardError => err @err.puts "ERROR: While executing genfrag ... (#{err.class})" @err.puts " #{err.to_s}" @err.puts %Q( #{err.backtrace.join("\n\t")}) exit 1 end |
#help ⇒ Object
Show the toplevel help message.
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# File 'lib/genfrag/app.rb', line 65 def help @out.puts <<-MSG GenFrag allows for rapid in-silico searching of fragments cut by different restriction enzymes in large nucleotide acid databases, followed by matching specificity adapters which allow a further data reduction when looking for differential expression of genes and markers. Usage: genfrag -h/--help genfrag -V/--version genfrag command [options] [arguments] Examples: genfrag index -f example.fasta --RE5 BstYI --RE3 MseI genfrag search -f example.fasta --RE5 BstYI --RE3 MseI --adapter5 ct Commands: genfrag index initialize the index genfrag search search FIXME genfrag info show information about FIXME Further Help: Each command has a '--help' option that will provide detailed information for that command. http://genfrag.rubyforge.org/ MSG nil end |