Class: MiGA::Cli::Action::TaxSet

Inherits:
MiGA::Cli::Action show all
Defined in:
lib/miga/cli/action/tax_set.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_set.rb', line 7

def parse_cli
  cli.parse do |opt|
    cli.opt_object(opt, [:project, :dataset_opt])
    opt.on(
      '-s', '--tax-string STRING',
      'String corresponding to the taxonomy of the dataset',
      'A space-delimited set of \'rank:name\' pairs'
    ) { |v| cli[:taxstring] = v }
    opt.on(
      '-t', '--tax-file PATH',
      '(Mandatory unless -D and -s are provided)',
      'Tab-delimited file containing datasets taxonomy',
      'Each row corresponds to a datasets and each column to a rank',
      'The first row must be a header with the rank names,',
      'and the first column must contain dataset names'
    ) { |v| cli[:taxfile] = v }
  end
end

#perform ⇒ Object 



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# File 'lib/miga/cli/action/tax_set.rb', line 26

def perform
  p = cli.load_project
  if !cli[:taxfile].nil?
    cli.say 'Reading tax-file and registering taxonomy'
    tfh = File.open(cli[:taxfile], 'r')
    header = nil
    tfh.each_line do |ln|
      next if ln =~ /^\s*?$/

      r = ln.chomp.split(/\t/, -1)
      dn = r.shift
      if header.nil?
        header = r
        next
      end
      d = p.dataset(dn)
      if d.nil?
        warn "Impossible to find dataset at line #{$.}: #{dn}. Ignoring..."
        next
      end
      d.metadata[:tax] = Taxonomy.new(r, header)
      d.save
      cli.say "o #{d.name} registered"
    end
    tfh.close
  else
    cli.ensure_par({ dataset: '-D', taxstring: '-s' },
                   '%<flag>s is mandatory unless -t is provided')
    cli.say 'Registering taxonomy'
    d = cli.load_dataset
    d.metadata[:tax] = Taxonomy.new(cli[:taxstring])
    d.save
  end
end