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, #finalize_tasks, #generic_perform, #impose_limit, #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 }
  cli.opt_flag(
    opt, 'legacy-name',
    'Use dataset names based on chromosome entries instead of assembly',
    :legacy_name
  )
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
end

#parse_csv_as_datasets(doc) ⇒ Object 



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# File 'lib/miga/cli/action/download/ncbi.rb', line 69

def parse_csv_as_datasets(doc)
  ds = {}
  CSV.parse(doc, headers: true).each do |r|
    asm = r['assembly']
    next if asm.nil? || asm.empty? || asm == '-'

    rep = remote_row_replicons(r)
    n = remote_row_name(r, rep, asm)

    # Register for download
    ds[n] = {
      ids: [asm], db: :assembly, universe: :ncbi,
      md: {
        type: :genome, ncbi_asm: asm, strain: r['strain']
      }
    }
    ds[n][:md][:ncbi_nuccore] = rep.join(',') unless rep.nil?
    unless r['release_date'].nil?
      ds[n][:md][:release_date] = Time.parse(r['release_date']).to_s
    end
  end
  ds
end

#remote_list ⇒ Object 



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# File 'lib/miga/cli/action/download/ncbi.rb', line 54

def remote_list
  doc =
    if cli[:ncbi_table_file]
      cli.say 'Reading genome list from file'
      File.open(cli[:ncbi_table_file], 'r')
    else
      cli.say 'Downloading genome list'
      url = remote_list_url
      MiGA::RemoteDataset.download_url(url)
    end
  ds = parse_csv_as_datasets(doc)
  doc.close if cli[:ncbi_table_file]
  ds
end

#remote_list_url ⇒ Object 



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# File 'lib/miga/cli/action/download/ncbi.rb', line 114

def remote_list_url
  url_base = 'https://www.ncbi.nlm.nih.gov/genomes/solr2txt.cgi?'
  url_param = {
    q: '[display()].' \
      'from(GenomeAssemblies).' \
      'usingschema(/schema/GenomeAssemblies).' \
      'matching(tab==["Prokaryotes"] and q=="' \
        "#{cli[:taxon]&.tr('"', "'")}\"",
    fields: 'organism|organism,assembly|assembly,replicons|replicons,' \
      'level|level,release_date|release_date,strain|strain',
    nolimit: 'on'
  }
  if cli[:reference]
    url_param[:q] += ' and refseq_category==["representative"]'
  else
    status = {
      complete: 'Complete',
      chromosome: ' Chromosome', # <- The leading space is *VERY* important!
      scaffold: 'Scaffold',
      contig: 'Contig'
    }.map { |k, v| '"' + v + '"' if cli[k] }.compact.join(',')
    url_param[:q] += ' and level==[' + status + ']'
  end
  url_param[:q] += ')'
  url_base + URI.encode_www_form(url_param)
end

#remote_row_name(r, rep, asm) ⇒ Object 



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# File 'lib/miga/cli/action/download/ncbi.rb', line 102

def remote_row_name(r, rep, asm)
  return r['#organism'].miga_name if cli[:legacy_name] && cli[:reference]

  if cli[:legacy_name] && ['Complete', ' Chromosome'].include?(r['level'])
    acc = rep.nil? ? '' : rep.first
  else
    acc = asm
  end
  acc.gsub!(/\.\d+\Z/, '') unless cli[:add_version]
  "#{r['#organism']}_#{acc}".miga_name
end

#remote_row_replicons(r) ⇒ Object 



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# File 'lib/miga/cli/action/download/ncbi.rb', line 93

def remote_row_replicons(r)
  return if r['replicons'].nil?

  r['replicons']
    .split('; ')
    .map { |i| i.gsub(/.*:/, '') }
    .map { |i| i.gsub(%r{/.*}, '') }
end

#sanitize_cli ⇒ Object 



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# File 'lib/miga/cli/action/download/ncbi.rb', line 44

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