Class: MiGA::Cli::Action::TaxDist

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

#cannid(a, b) ⇒ Object 



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

def cannid(a, b)
  (a > b ? [b, a] : [a, b]).join('-')
end

#parse_cli ⇒ Object 



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# File 'lib/miga/cli/action/tax_dist.rb', line 9

def parse_cli
  cli.parse do |opt|
    cli.opt_object(opt, [:project])
    cli.opt_filter_datasets(opt)
    opt.on(
      '-i', '--index FILE',
      'Pre-calculated tax-index (in tabular format) to be used',
      'If passed, dataset filtering arguments are ignored'
    ) { |v| cli[:index] = v }
    opt.on(
      '-m', '--metric STR',
      'Distance metric used to evaluate the distribution',
      'By default: AAI for genomes projects, ANI for clade projects'
    ) { |v| cli[:metric] = v.downcase }
  end
end

#perform ⇒ Object 



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# File 'lib/miga/cli/action/tax_dist.rb', line 30

def perform
  dist = read_distances
  Dir.mktmpdir do |dir|
    tab = get_tab_index(dir)
    dist = traverse_taxonomy(tab, dist)
  end

  cli.say 'Generating report'
  dist.keys.each do |k|
    dist[k][5] = dist[k][4].reverse.join(' ')
    dist[k][4] = dist[k][4].first
    puts (k.split('-') + dist[k]).join("\t")
  end
end