Class: MiGA::Cli::Action::TaxIndex

Inherits:
MiGA::Cli::Action show all
Defined in:
lib/miga/cli/action/tax_index.rb

Constant Summary

Constants included from MiGA

MiGA::CITATION, VERSION, VERSION_DATE, VERSION_NAME

Instance Attribute Summary

Attributes inherited from MiGA::Cli::Action

#cli

Attributes included from MiGA::Common::Net

#remote_connection_uri

Instance Method Summary collapse

Methods inherited from MiGA::Cli::Action

#complete, #empty_action, #initialize, #launch, load, #name

Methods inherited from MiGA

CITATION, CITATION_ARRAY, DEBUG, DEBUG_OFF, DEBUG_ON, DEBUG_TRACE_OFF, DEBUG_TRACE_ON, FULL_VERSION, LONG_VERSION, VERSION, VERSION_DATE, #advance, debug?, debug_trace?, initialized?, #like_io?, #num_suffix, rc_path, #result_files_exist?, #say

Methods included from MiGA::Common::Path

#root_path, #script_path

Methods included from MiGA::Common::Format

#clean_fasta_file, #seqs_length, #tabulate

Methods included from MiGA::Common::Net

#download_file_ftp, #http_request, #known_hosts, #main_server, #net_method, #normalize_encoding, #remote_connection

Methods included from MiGA::Common::SystemCall

#run_cmd, #run_cmd_opts

Constructor Details

This class inherits a constructor from MiGA::Cli::Action

Instance Method Details

#parse_cli ⇒ Object 



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# File 'lib/miga/cli/action/tax_index.rb', line 8

def parse_cli
  cli.defaults = { format: :json }
  cli.parse do |opt|
    cli.opt_object(opt, [:project])
    opt.on(
      '-i', '--index PATH',
      '(Mandatory) File to create with the index'
    ) { |v| cli[:index] = v }
    opt.on(
      '-f', '--format STRING',
      "Format of the index file, by default: #{cli[:format]}",
      'Supported: json, tab.'
    ) { |v| cli[:format] = v.downcase.to_sym }
    cli.opt_filter_datasets(opt)
  end
end

#perform ⇒ Object 



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# File 'lib/miga/cli/action/tax_index.rb', line 25

def perform
  cli.ensure_par(index: '-i')
  ds = cli.load_and_filter_datasets

  cli.say 'Indexing taxonomy'
  tax_index = MiGA::TaxIndex.new
  ds.each_with_index do |d, i|
    cli.advance('Datasets:', i, ds.size, false)
    tax_index << d unless d.metadata[:tax].nil?
  end
  cli.say ''

  cli.say 'Saving index'
  File.open(cli[:index], 'w') do |fh|
    case cli[:format]
    when :json
      fh.print tax_index.to_json
    when :tab
      fh.print tax_index.to_tab
    else
      raise "Unsupported output format: #{cli[:format]}"
    end
  end
end