Class: Bio::SRA::Accession

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/sra/sra.rb

Constant Summary collapse

ACCESSION_TO_TYPE =

valid_in_type <- c(SRA = “submission”, ERA = “submission”, DRA = “submission”, SRP = “study”, ERP = “study”, DRP = “study”, SRS = “sample”, ERS = “sample”, DRS = “sample”, SRX = “experiment”, ERX = “experiment”, DRX = “experiment”, SRR = “run”, ERR = “run”, DRR = “run”)

{
  'SRA' => Bio::SRA::SUBMISSION,
  'ERA' => Bio::SRA::SUBMISSION,
  'DRA' => Bio::SRA::SUBMISSION,
  'SRP' => Bio::SRA::STUDY,
  'ERP' => Bio::SRA::STUDY,
  'DRP' => Bio::SRA::STUDY,
  'SRS' => Bio::SRA::SAMPLE,
  'ERS' => Bio::SRA::SAMPLE,
  'DRS' => Bio::SRA::SAMPLE,
  'SRX' => Bio::SRA::EXPERIMENT,
  'ERX' => Bio::SRA::EXPERIMENT,
  'DRX' => Bio::SRA::EXPERIMENT,
  'SRR' => Bio::SRA::RUN,
  'ERR' => Bio::SRA::RUN,
  'DRR' => Bio::SRA::RUN,
}
TYPE_TO_COLUMN = 
{
  Bio::SRA::SUBMISSION => :submission_accession,
  Bio::SRA::STUDY => :study_accession,
  Bio::SRA::SAMPLE => :sample_accession,
  Bio::SRA::EXPERIMENT => :experiment_accession,
  Bio::SRA::RUN => :run_accession,
}
@@log = 
Bio::Log::LoggerPlus['bio-sra']

Class Method Summary collapse

Class Method Details

.accession_to_column_name(accession) ⇒ Object

Given an accession, return the column name it in the SRA table that contains it as a symbol. e.g. accession_to_column_name(‘SRR617581’) => :run_accession



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# File 'lib/bio/sra/sra.rb', line 54

def self.accession_to_column_name(accession)
  TYPE_TO_COLUMN[classify_accession_type(accession)]
end

.classify_accession_type(accession) ⇒ Object 



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# File 'lib/bio/sra/sra.rb', line 43

def self.classify_accession_type(accession)
  type = ACCESSION_TO_TYPE[accession[0..2]]
  if type.nil?
    raise "Unrecognised accession string '#{accession}'"
  end
  @@log.debug "Classified #{accession} as SRA type '#{type}'" if @@log.debug?
  return type
end

.format_symbol_to_extension(format_symbol) ⇒ Object 



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# File 'lib/bio/sra/sra.rb', line 58

def self.format_symbol_to_extension(format_symbol)
  non_standard_extensions = {
    :sralite => '.lite.sra',
    :fastq_gz => '.fastq.gz',
  }
  style = format_symbol_to_standard_text format_symbol

  # Default extension is the same as the format
  style_extension = non_standard_extensions[format_symbol]
  style_extension ||= ".#{style}"

  return style_extension
end

.format_symbol_to_standard_text(format_symbol) ⇒ Object 



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# File 'lib/bio/sra/sra.rb', line 72

def self.format_symbol_to_standard_text(format_symbol)
  formats = {
    :sralite => 'litesra',
    :sra => 'sra',
    :fastq_gz => 'fastq',
    :sff => 'sff'
  }
  style = formats[format_symbol]
  if style.nil?
    raise "Unexpected download format detected #{format_symbol}, I need one of '#{formats.keys.join(', ')}'"
  end
  return style
end

.run_download_url(run_accession, options = {}) ⇒ Object

Return the URL where a run can be downloaded. Only works if the accession is a run accession e.g. SRR000002 or DRR000002. To get run accessions from other accession type e.g. SRP000002, try Bio::SRA::Sra

Options: :source: either :ncbi (default), or :ebi :format: either :sralite (default if :source if :ncbi), :fastq_gz (default if :source is :ebi), :sra :layout: either :single (default), :paired1, or :paired2. :paired1 for the first half, :paired2 for the second half. Only required when :source => :ebi, otherwise not used



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# File 'lib/bio/sra/sra.rb', line 92

def self.run_download_url(run_accession, options={})
  options ||= {}
  options[:source] ||= :ncbi
  if options[:source] == :ebi
    options[:format] ||= :fastq
    options[:layout] ||= :single
  else
    options[:format] ||= :sralite #default to sralite
  end


  type = classify_accession_type(run_accession)
  unless type == Bio::SRA::RUN
    raise "Unexpected type of accession for '#{run_accession}': Expected #{Bio::SRA::RUN} but was #{type}"
  end

  style = format_symbol_to_standard_text options[:format]
  style_extension = format_symbol_to_extension options[:format]

  if options[:source] == :ncbi
    # e.g.
    # ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/litesra/DRR/DRR000/DRR000002/DRR000002/DRR000002.lite.sra
    [
      "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun",
      style,
      run_accession[0..2],
      run_accession[0..5],
      run_accession,
      "#{run_accession}#{style_extension}"
    ].join('/')
  elsif options[:source] == :ebi
    unless style == 'fastq'
      raise "Unexpected format for download detected #{options[:format]} in combination with :source => :ebi. Require :fastq_gz"
    end
    ok_layouts = [:single, :paired1, :paired2]
    unless ok_layouts.include?(options[:layout])
      raise "Unexpected layout for download detected #{options[:layout]} in combination with :source => :ebi. Require on of #{ok_layouts.join(', ')}."
    end
    # e.g. for paired ended
    # ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR069/SRR069027/SRR069027_1.fastq.gz
    # e.g. for single end
    # ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR404/SRR404303/SRR404303.fastq.gz
    most = [
      'ftp://ftp.sra.ebi.ac.uk/vol1/',
      style,
      run_accession[0..5],
      run_accession,
    ]
    if options[:layout] == :single
      most.push "#{run_accession}#{style_extension}"
    elsif options[:layout] == :format1
      most.push "#{run_accession}_1#{style_extension}"
    elsif options[:layout] == :format2
      most.push "#{run_accession}_2#{style_extension}"
    end
    return most.join('/')
  end
end