Class: EuPathDBSpeciesData

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

Overview

A class dedicated to recording ‘administrative’ data about the databases, answering questions such as “which species are recorded in ToxoDB?” for instance.

It is also meant for dealing with locally cached version of the files, where all the data is stored in a base directory with a specified structure.

TODO: functions for the info and the local caching should probably be separated into separate classes, and the directory structure of the local versions shouldn’t be forced on the user.

Constant Summary collapse

SOURCE_VERSIONS = 
{
  'PlasmoDB' => '8.2',
  'ToxoDB' => '7.2',
  'CryptoDB' => '4.6',
  'PiroplasmaDB' => '1.1',
  'FungiDB' => '1.0',
  'TriTrypDB' => '4.0',
}
DATABASES = 
SOURCE_VERSIONS.keys
@@data = 
{
  ## PlasmoDB
  'Plasmodium falciparum' => {
    :name => 'Plasmodium falciparum',
    :source => 'PlasmoDB',
    :fasta_file_species_name => 'Plasmodium_falciparum_3D7',
    :sequencing_centre_abbreviation => 'psu',
    :behind_usage_policy => true,
  },
  'Plasmodium yoelii' => {
    :directory => 'yoelii',
    :name => 'Plasmodium yoelii',
    :sequencing_centre_abbreviation => 'TIGR',
    :fasta_file_species_name => 'Plasmodium_yoelii_yoelii_str._17XNL',
    :proteins_fasta_filename => lambda {|version| "PyoeliiAnnotatedProteins_PlasmoDB-#{version}.fasta"},
    #:transcripts_fasta_filename => lambda {|version| "PyoeliiAllTranscripts_PlasmoDB-#{version}.fasta"},
    :source => 'PlasmoDB'
  },
  'Plasmodium vivax' => {
    :name => 'Plasmodium vivax',
    :sequencing_centre_abbreviation => 'gb',
    :fasta_file_species_name => 'Plasmodium_vivax_SaI-1',
    :proteins_fasta_filename => lambda {|version| "PvivaxAnnotatedProteins_PlasmoDB-#{version}.fasta"},
    :source => 'PlasmoDB'
  },
  'Plasmodium berghei' => {
    :name => 'Plasmodium berghei',
    :sequencing_centre_abbreviation => 'psu',
    :fasta_file_species_name => 'Plasmodium_berghei_str._ANKA',
    :proteins_fasta_filename => lambda {|version| "PbergheiAnnotatedProteins_PlasmoDB-#{version}.fasta"},
    #:transcripts_fasta_filename => lambda {|version| "PbergheiAllTranscripts_PlasmoDB-#{version}.fasta"},
    :source => 'PlasmoDB'
  },
  'Plasmodium chabaudi' => {
    :name => 'Plasmodium chabaudi',
    :sequencing_centre_abbreviation => 'psu',
    :fasta_file_species_name => 'Plasmodium_chabaudi_chabaudi',
    :proteins_fasta_filename => lambda {|version| "PchabaudiAnnotatedProteins_PlasmoDB-#{version}.fasta"},
    :source => 'PlasmoDB',
    :behind_usage_policy => true,
  },
  'Plasmodium knowlesi' => {
    :name => 'Plasmodium knowlesi',
    :sequencing_centre_abbreviation => 'psu',
    :fasta_file_species_name => 'Plasmodium_knowlesi_strain_H',
    :source => 'PlasmoDB',
    :behind_usage_policy => true,
  },
  ## ToxoDB
  'Neospora caninum' => {
    :name => 'Neospora caninum',
    :sequencing_centre_abbreviation => 'psu',
    :fasta_file_species_name => 'Neospora_caninum',
    :database_download_folder => 'NeosporaCaninum',
    :representative_strain_name => 'NeosporaCaninum',
    :proteins_fasta_filename => lambda {|version| "NeosporaCaninumAnnotatedProteins_ToxoDB-#{version}.fasta"},
    :transcripts_fasta_filename => lambda {|version| "NeosporaCaninumAnnotatedTranscripts_ToxoDB-#{version}.fasta"},
    :source => 'ToxoDB',
    :behind_usage_policy => true,
  },
  'Eimeria tenella' => {
    :name => 'Eimeria tenella',
    :sequencing_centre_abbreviation => 'GeneDB',
    :fasta_file_species_name => 'EtenellaHoughton',
    :source => 'ToxoDB',
    :database_download_folder => 'EtenellaHoughton',
    :behind_usage_policy => true,
    :fasta_file_species_name => 'Eimeria_tenella_str._Houghton',
  },
  'Toxoplasma gondii' => {
    :name => 'Toxoplasma gondii',
    :sequencing_centre_abbreviation => 'gb',
    :fasta_file_species_name => 'Toxoplasma_gondii_ME49',
    :database_download_folder => 'TgondiiME49',
    :gene_information_filename => lambda {|version| "TgondiiME49Gene_ToxoDB-#{version}.txt"},
    :proteins_fasta_filename => lambda {|version| "TgondiiME49AnnotatedProteins_ToxoDB-#{version}.fasta"},
    :transcripts_fasta_filename => lambda {|version| "TgondiiME49AnnotatedTranscripts_ToxoDB-#{version}.fasta"},
    :gff_filename => lambda {|version| "TgondiiME49_ToxoDB-#{version}.gff"},
    :genomic_fasta_filename => lambda {|version| "TgondiiME49Genomic_ToxoDB-#{version}.fasta"},
    :source => 'ToxoDB'
  },
  ## CryptoDB
  'Cryptosporidium parvum' => {
    :name => 'Cryptosporidium parvum',
    :sequencing_centre_abbreviation => 'gb',
    :fasta_file_species_name => 'Cryptosporidium_parvum',
    :proteins_fasta_filename => lambda {|version| "CparvumAnnotatedProteins_CryptoDB-#{version}.fasta"},
    :transcripts_fasta_filename => lambda {|version| "CparvumAnnotatedTranscripts_CryptoDB-#{version}.fasta"},
    #:gff_filename => lambda {|version| "c_parvum_iowa_ii.gff"}, #changed as of version 4.3
    :source => 'CryptoDB'
  },
  'Cryptosporidium hominis' => {
    :name => 'Cryptosporidium hominis',
    :sequencing_centre_abbreviation => 'gb',
    :fasta_file_species_name => 'Cryptosporidium_hominis',
    :proteins_fasta_filename => lambda {|version| "ChominisAnnotatedProteins_CryptoDB-#{version}.fasta"},
    :transcripts_fasta_filename => lambda {|version| "ChominisAnnotatedTranscripts_CryptoDB-#{version}.fasta"},
    #:gff_filename => lambda {|version| "c_hominis_tu502.gff"}, #changed as of version 4.3
    :source => 'CryptoDB'
  },
  'Cryptosporidium muris' => {
    :name => 'Cryptosporidium muris',
    :sequencing_centre_abbreviation => 'gb',
    :fasta_file_species_name => 'Cryptosporidium_muris',
    :proteins_fasta_filename => lambda {|version| "CmurisAnnotatedProteins_CryptoDB-#{version}.fasta"},
    :transcripts_fasta_filename => lambda {|version| "CmurisAnnotatedTranscripts_CryptoDB-#{version}.fasta"},
    #:gff_filename => lambda {|version| "c_muris.gff"}, #changed as of version 4.3
    :source => 'CryptoDB'
  },
  ## PiroplasmaDB
  'Theileria annulata' => {
    :name => 'Theileria annulata',
    :database_download_folder => 'TannulataAnkara',
    :sequencing_centre_abbreviation => 'Genbank',
    :fasta_file_species_name => 'Theileria_annulata_strain_Ankara',
    :source => 'PiroplasmaDB',
  },
  'Theileria parva' => {
    :name => 'Theileria parva',
    :database_download_folder => 'TparvaMuguga',  
    :sequencing_centre_abbreviation => 'Genbank',
    :fasta_file_species_name => 'Theileria_parva_strain_Muguga',
    :source => 'PiroplasmaDB', 
  },
  'Babesia bovis' => {
    :name => 'Babesia bovis',
    :database_download_folder => 'BbovisT2Bo',
    :representative_strain_name => 'BbovisT2Bo',
    :sequencing_centre_abbreviation => 'Genbank',
    :fasta_file_species_name => 'Babesia_bovis_T2Bo',
    :source => 'PiroplasmaDB',
  },
  ## FungiDB
  'Candida albicans' => {
    :name => 'Candida albicans',
    :database_download_folder => 'Candida_albicans_SC5314',
    :sequencing_centre_abbreviation => 'CGD',
    :fasta_file_species_name => 'Candida_albicans_SC5314',
    :source => 'FungiDB',
  },
  ## TriTrypDB
  'Trypanosoma brucei' => {
    :name => 'Trypanosoma brucei',
    :sequencing_centre_abbreviation => 'GeneDB',
    :source => 'TriTrypDB',
    :representative_strain_name => 'TbruceiTreu927',
    :fasta_file_species_name => 'Trypanosoma_brucei_TREU927',
  },
}

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(nickname, base_data_directory = nil, database_version = nil) ⇒ EuPathDBSpeciesData

Create a new object about one particular species. The species can be specified by a nickname, which is either the full binomal name of the specie e.g. “Plasmodium falciparum”, or by simply the second part (the species name without the genus name) e.g. ‘falciparum’.

base_data_directory is the directory where locally cached version of the downloaded files are stored.

Raises:

  • (Exception) 


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# File 'lib/eupathdb_species_data.rb', line 190

def initialize(nickname, base_data_directory=nil, database_version=nil)
  @species_data = @@data[nickname] # try the full name
  @species_data ||= @@data[nickname.capitalize.gsub('_',' ')] #try replacing underscores
  if @species_data.nil? # try using just the second word
    splits = nickname.split(' ')
    if splits.length == 2
      @species_data = @@data[splits[1]]
    end
  end
  raise Exception, "Couldn't find species data for #{nickname}" unless @species_data
  
  @base_data_directory = base_data_directory
  
  # record out what version of the db we are looking at, otherwise default
  @database_version = database_version
  @database_version ||= SOURCE_VERSIONS[@species_data[:source]]
end

Dynamic Method Handling

This class handles dynamic methods through the method_missing method

#method_missing(symbol) ⇒ Object 



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# File 'lib/eupathdb_species_data.rb', line 208

def method_missing(symbol)
  answer = @species_data[symbol]
  return answer unless answer.nil?
  super
end

Class Method Details

.download(base_download_directory, database_name = nil) ⇒ Object

Download all the data files from all the EuPathDB databases, or just one single database. Requires wget to be available on the command line



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# File 'lib/eupathdb_species_data.rb', line 370

def self.download(base_download_directory, database_name=nil)
  # by default, download everything
  if database_name.nil?
    EuPathDBSpeciesData::DATABASES.each do |d|
      download base_download_directory, d
    end
  else
    # Download the new files from the relevant database
    EuPathDBSpeciesData.species_data_from_database(database_name, base_download_directory).each do |spd|
      spd.directories_for_mkdir.each do |directory|
        unless File.exists?(directory)
          Dir.mkdir(directory)
        end
      end
      
      Dir.chdir(spd.local_download_directory) do
        p spd.eu_path_db_fasta_download_directory
          
        # protein
        unless File.exists?(spd.protein_fasta_filename)
          `wget #{spd.eu_path_db_fasta_download_directory}/#{spd.protein_fasta_filename}`
        end
        # gff
        unless File.exists?(spd.gff_filename)
          `wget #{spd.eu_path_db_gff_download_directory}/#{spd.gff_filename}`
        end
        # transcripts
        unless File.exists?(spd.transcript_fasta_filename)
          `wget #{spd.eu_path_db_fasta_download_directory}/#{spd.transcript_fasta_filename}`
        end
        # gene information table
        unless File.exists?(spd.gene_information_filename)
          `wget '#{spd.eu_path_db_txt_download_directory}/#{spd.gene_information_filename}'`
        end
        # genomic
        unless File.exists?(spd.genomic_fasta_filename)
          `wget '#{spd.eu_path_db_fasta_download_directory}/#{spd.genomic_fasta_filename}'`
        end
      end
    end
  end
end

.species_data_from_database(database_name, base_download_directory = nil) ⇒ Object

Return a list of the species names that are included in the EuPathDB database



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# File 'lib/eupathdb_species_data.rb', line 358

def self.species_data_from_database(database_name, base_download_directory=nil)
  species = @@data.select {|name, info|
    info[:source].downcase == database_name.downcase and
    name == info[:name] #only allow ones that are fully specified - not shortcut ones
  }
  species.collect do |name_info|
    EuPathDBSpeciesData.new(name_info[0], base_download_directory)
  end
end

Instance Method Details

#database ⇒ Object 



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# File 'lib/eupathdb_species_data.rb', line 296

def database
  @species_data[:source]
end

#directories_for_mkdir ⇒ Object

an array of directory names. mkdir is called on each of them in order, otherwise mkdir throws errors because there isn’t sufficient folders to build on.



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# File 'lib/eupathdb_species_data.rb', line 338

def directories_for_mkdir
  if @base_data_directory.nil?
    raise Exception, "Unable to generate directories when @base_data_directory is not set"
  end
  
  s = @species_data
  components = [
    @base_data_directory,
  s[:name],
    'genome',
  s[:source],
  @database_version,
  ]
  
   (0..components.length-1).collect do |i|
    components[0..i].join('/')
  end
end

#eu_path_db_download_directory ⇒ Object 



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# File 'lib/eupathdb_species_data.rb', line 300

def eu_path_db_download_directory
  "http://#{database.downcase}.org/common/downloads/release-#{@database_version}/#{one_word_name}"
end

#eu_path_db_fasta_download_directory ⇒ Object 



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# File 'lib/eupathdb_species_data.rb', line 304

def eu_path_db_fasta_download_directory
  path = "#{eu_path_db_download_directory}/fasta"
  path = "#{path}/data" if @species_data[:behind_usage_policy]
  path
end

#eu_path_db_gff_download_directory ⇒ Object 



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# File 'lib/eupathdb_species_data.rb', line 310

def eu_path_db_gff_download_directory
  path = "#{eu_path_db_download_directory}/gff"
  path = "#{path}/data" if @species_data[:behind_usage_policy]
  path
end

#eu_path_db_txt_download_directory ⇒ Object 



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# File 'lib/eupathdb_species_data.rb', line 316

def eu_path_db_txt_download_directory
  path = "#{eu_path_db_download_directory}/txt"
  path = "#{path}/data" if @species_data[:behind_usage_policy]
  path
end

#gene_information_filename ⇒ Object 



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# File 'lib/eupathdb_species_data.rb', line 233

def gene_information_filename
  f = @species_data[:gene_information_filename]
  if f
    "#{f.call(version)}"
  else      # TgondiiME49Gene_ToxoDB-5.2.txt.gz
    # PfalciparumGene_PlasmoDB-6.1.txt.gz
    "#{representative_strain_name}Gene_#{database}-#{version}.txt"
  end
end

#gene_information_gzfile_filename ⇒ Object

The path to the EuPathDB gene information table (stored as a gzip)



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# File 'lib/eupathdb_species_data.rb', line 220

def gene_information_gzfile_filename
  "#{gene_information_filename}.gz"
end

#gene_information_gzfile_path ⇒ Object

The path to the EuPathDB gene information table (stored as a gzip)



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# File 'lib/eupathdb_species_data.rb', line 215

def gene_information_gzfile_path
  "#{local_download_directory}/#{gene_information_gzfile_filename}"
end

#gene_information_path ⇒ Object 



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# File 'lib/eupathdb_species_data.rb', line 224

def gene_information_path
  "#{local_download_directory}/#{gene_information_filename}"
end

#genomic_fasta_filename ⇒ Object 



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# File 'lib/eupathdb_species_data.rb', line 275

def genomic_fasta_filename
  genomic = @species_data[:genomic_fasta_filename]
  if genomic
    return "#{genomic.call(version)}"
  else
    return "#{representative_strain_name}Genomic_#{database}-#{version}.fasta"
  end
end

#gff_filename ⇒ Object 



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# File 'lib/eupathdb_species_data.rb', line 284

def gff_filename
  if @species_data[:gff_filename]
    return @species_data[:gff_filename].call(version)
  else
    return "#{representative_strain_name}_#{database}-#{version}.gff"
  end
end

#gff_path ⇒ Object 



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# File 'lib/eupathdb_species_data.rb', line 292

def gff_path
  File.join(local_download_directory,gff_filename)
end

#local_download_directory ⇒ Object 



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# File 'lib/eupathdb_species_data.rb', line 330

def local_download_directory
  s = @species_data
  "#{@base_data_directory}/#{s[:name]}/genome/#{s[:source]}/#{@database_version}"
end

#one_word_name ⇒ Object

Plasmodium chabaudi => Pchabaudi



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# File 'lib/eupathdb_species_data.rb', line 323

def one_word_name
  return @species_data[:database_download_folder] unless @species_data[:database_download_folder].nil?
  splits = @species_data[:name].split(' ')
  raise unless splits.length == 2
  return "#{splits[0][0..0]}#{splits[1]}"
end

#protein_blast_database_path ⇒ Object 



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# File 'lib/eupathdb_species_data.rb', line 259

def protein_blast_database_path
  "/blastdb/#{protein_fasta_filename}"
end

#protein_fasta_file_iterator ⇒ Object 



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# File 'lib/eupathdb_species_data.rb', line 413

def protein_fasta_file_iterator
  Bio::EuPathDB::FastaParser.new(fasta_file_species_name, protein_fasta_path)
end

#protein_fasta_filename ⇒ Object 



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# File 'lib/eupathdb_species_data.rb', line 247

def protein_fasta_filename
  if @species_data[:proteins_fasta_filename]
    return "#{@species_data[:proteins_fasta_filename].call(version)}"
  else
    return "#{representative_strain_name}AnnotatedProteins_#{database}-#{version}.fasta"
  end
end

#protein_fasta_path ⇒ Object 



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# File 'lib/eupathdb_species_data.rb', line 255

def protein_fasta_path
  return File.join(local_download_directory,protein_fasta_filename)
end

#representative_strain_name ⇒ Object 



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# File 'lib/eupathdb_species_data.rb', line 228

def representative_strain_name
  return @species_data[:representative_strain_name] unless @species_data[:representative_strain_name].nil?
  return one_word_name
end

#transcript_fasta_filename ⇒ Object 



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# File 'lib/eupathdb_species_data.rb', line 263

def transcript_fasta_filename
  if @species_data[:transcripts_fasta_filename]
    return "#{@species_data[:transcripts_fasta_filename].call(version)}"
  else
    return "#{representative_strain_name}AnnotatedTranscripts_#{database}-#{version}.fasta"
  end
end

#transcript_fasta_path ⇒ Object 



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# File 'lib/eupathdb_species_data.rb', line 271

def transcript_fasta_path
  File.join(local_download_directory,transcript_fasta_filename)
end

#version ⇒ Object 



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# File 'lib/eupathdb_species_data.rb', line 243

def version
  @database_version
end