Module: MiGA::Cli::Action::Download::Ncbi

Includes:
Base
Included in:
NcbiGet
Defined in:
lib/miga/cli/action/download/ncbi.rb

Overview

Helper module including download functions for the ncbi_get action

Instance Method Summary collapse

Methods included from Base

#cli_base_flags, #cli_filters, #cli_save_actions, #discard_excluded, #download_entries, #exclude_newer, #finalize_tasks, #generic_perform, #impose_limit, #load_ncbi_taxonomy_dump, #load_tasks, #save_entry, #unlink_entries

Instance Method Details

#cli_name_modifiers(opt) ⇒ Object 



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# File 'lib/miga/cli/action/download/ncbi.rb', line 31

def cli_name_modifiers(opt)
  opt.on(
    '--no-version-name',
    'Do not add sequence version to the dataset name',
    'Only affects --complete and --chromosome'
  ) { |v| cli[:add_version] = v }
  # For backwards compatibility
  opt.on('--legacy-name', '::HIDE::') do
    warn 'Deprecated flag --legacy-name ignored'
  end
end

#cli_task_flags(opt) ⇒ Object 



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# File 'lib/miga/cli/action/download/ncbi.rb', line 11

def cli_task_flags(opt)
  cli.opt_flag(
    opt, 'reference',
    'Download all reference genomes (ignore any other status)'
  )
  cli.opt_flag(opt, 'complete', 'Download complete genomes')
  cli.opt_flag(opt, 'chromosome', 'Download complete chromosomes')
  cli.opt_flag(opt, 'scaffold', 'Download genomes in scaffolds')
  cli.opt_flag(opt, 'contig', 'Download genomes in contigs')
  opt.on('--all', 'Download all genomes (in any status)') do
    cli[:complete] = true
    cli[:chromosome] = true
    cli[:scaffold] = true
    cli[:contig] = true
  end
  opt.on('--ncbi-list-json STRING', '::HIDE::') do |v|
    cli[:ncbi_list_json] = v
  end
end

#parse_reports_as_datasets(reports) ⇒ Object 



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# File 'lib/miga/cli/action/download/ncbi.rb', line 112

def parse_reports_as_datasets(reports)
  ds = {}
  reports.each do |r|
    asm = r[:accession]
    next if asm.nil? || asm.empty? || asm == '-'

    # Register for download
    n = remote_report_name(r, asm)
    ds[n] = {
      ids: [asm], db: :assembly, universe: :ncbi,
      md: {
        type: :genome, ncbi_asm: asm,
        strain: r.dig(:organism, :infraspecific_names, :strain)
      }
    }
    date = r.dig(:assembly_info, :release_date)
    ds[n][:md][:release_date] = Time.parse(date).to_s if date
    ds[n][:md][:ncbi_dataset] = r
  end
  ds
end

#read_ncbi_list_json(file) ⇒ Object 



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# File 'lib/miga/cli/action/download/ncbi.rb', line 83

def read_ncbi_list_json(file)
  cli.say "Reusing remote list: #{file}"
  list = {}
  n_tot = nil
  File.open(file, 'r') do |fh|
    n_tot = fh.gets.chomp.sub(/^# /, '').to_i
    fh.each_with_index do |ln, k|
      row = ln.chomp.split("\t", 2)
      list[row[0]] = MiGA::Json.parse(row[1], contents: true)
      cli.advance('Lines:', k, n_tot)
    end
    cli.say
  end
  return list
end

#remote_list ⇒ Object 



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# File 'lib/miga/cli/action/download/ncbi.rb', line 53

def remote_list
  if cli[:ncbi_list_json] && File.size?(cli[:ncbi_list_json])
    return read_ncbi_list_json(cli[:ncbi_list_json])
  end

  cli.say "Obtaining remote list of datasets"
  list  = {}
  query = remote_list_query
  loop do
    # Query the remote collection
    page = MiGA::Json.parse(
      MiGA::RemoteDataset.download(:ncbi_datasets, :genome, query, :json),
      contents: true
    )
    break unless page&.any? && page[:reports]&.any?

    # Process reports in this page
    list.merge!(parse_reports_as_datasets(page[:reports]))

    # Next page
    cli.advance('Datasets:', list.size, page[:total_count])
    break unless page[:next_page_token]
    query[:page_token] = page[:next_page_token]
  end
  cli.say

  write_ncbi_list_json(cli[:ncbi_list_json], list) if cli[:ncbi_list_json]
  list
end

#remote_list_query ⇒ Object 



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# File 'lib/miga/cli/action/download/ncbi.rb', line 142

def remote_list_query
  q = { taxons: [cli[:taxon]], filters: {} }
  if cli[:reference]
    q[:filters][:reference_only] = true
  else
    q[:assembly_level] = {
      contig: 'contig',
      scaffold: 'scaffold',
      chromosome: 'chromosome',
      complete: 'complete_genome'
    }.map { |k, v| '"' + v + '"' if cli[k] }.compact
  end
  q
end

#remote_report_name(r, asm) ⇒ Object 



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# File 'lib/miga/cli/action/download/ncbi.rb', line 134

def remote_report_name(r, asm)
  acc = "#{asm}"
  acc.gsub!(/\.\d+\Z/, '') unless cli[:add_version]
  org = r.dig(:organism, :organism_name)
  acc = "#{org}_#{acc}" if org
  acc.miga_name
end

#sanitize_cli ⇒ Object 



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# File 'lib/miga/cli/action/download/ncbi.rb', line 43

def sanitize_cli
  cli.ensure_par(taxon: '-T')
  tasks = %w[reference complete chromosome scaffold contig]
  unless tasks.any? { |i| cli[i.to_sym] }
    raise 'No action requested: pick at least one type of genome'
  end

  cli[:save_every] = 1 if cli[:dry]
end

#write_ncbi_list_json(file, list) ⇒ Object 



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# File 'lib/miga/cli/action/download/ncbi.rb', line 99

def write_ncbi_list_json(file, list)
  cli.say "Saving remote list: #{file}"
  File.open(file, 'w') do |fh|
    fh.puts('# %i' % list.size)
    kk = 0
    list.each do |k, v|
      fh.puts([k, MiGA::Json.generate_fast(v)].join("\t"))
      cli.advance('Datasets:', kk += 1, list.size)
    end
    cli.say
  end
end