Class: MiGA::Cli::Action::TaxTest

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

Constant Summary

Constants included from MiGA

MiGA::CITATION, VERSION, VERSION_DATE, VERSION_NAME

Instance Attribute Summary

Attributes inherited from MiGA::Cli::Action

#cli

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, #known_hosts, #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 



8
9
10
11
12
13
14
15
16
17
18
19
20
21
 
# File 'lib/miga/cli/action/tax_test.rb', line 8

def parse_cli
  cli.defaults = { test: 'both', ref_project: false }
  cli.parse do |opt|
    cli.opt_object(opt, [:project, :dataset])
    opt.on(
      '--ref-project',
      'Use the taxonomy from the reference project, not the current project'
    ) { |v| cli[:ref_project] = v }
    opt.on(
      '-t', '--test STRING',
      'Test to perform. Supported values: intax, novel, both'
    ) { |v| cli[:test] = v.downcase }
  end
end

#perform ⇒ Object 



23
24
25
26
27
28
29
30
31
32
33
34
 
# File 'lib/miga/cli/action/tax_test.rb', line 23

def perform
  d = cli.load_dataset
  cli.say 'Finding closest relative'
  cr = d.closest_relatives(1, cli[:ref_project])
  if cr.nil? or cr.empty?
    raise 'Action not supported for the project or dataset' if cr.nil?

    raise 'No close relatives found'
  else
    query_probability_distributions(d, cr[0])
  end
end