Module: Ensembl::FTP

Defined in:
lib/rbbt/sources/ensembl_ftp.rb

Constant Summary collapse

SERVER = 
"ftp.ensembl.org"
DOMAIN_SERVER = 
"ftp.ensemblgenomes.org"

Class Method Summary collapse

Class Method Details

._get_file(organism, table, extension) ⇒ Object 



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# File 'lib/rbbt/sources/ensembl_ftp.rb', line 83

def self._get_file(organism, table, extension)
  url = url_for(organism, table, extension)
  self._get_gz(url)
end

._get_gz(url) ⇒ Object 



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# File 'lib/rbbt/sources/ensembl_ftp.rb', line 75

def self._get_gz(url)
  begin
    CMD.cmd("wget '#{url}' -O  - | gunzip").read
  rescue
    CMD.cmd("wget '#{url}.bz2' -O  - | bunzip2 | gunzip").read
  end
end

.base_url(organism) ⇒ Object 



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# File 'lib/rbbt/sources/ensembl_ftp.rb', line 67

def self.base_url(organism)
  File.join("ftp://", ftp_url_for(organism) )
end

.ensembl_tsv(organism, table, key_field = nil, fields = nil, options = {}) ⇒ Object 



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# File 'lib/rbbt/sources/ensembl_ftp.rb', line 99

def self.ensembl_tsv(organism, table, key_field = nil, fields = nil, options = {})
  if key_field and fields
    all_fields = fields_for(organism, table)
    key_pos = all_fields.index key_field
    field_pos = fields.collect{|f| all_fields.index f}

    options[:key_field] = key_pos
    options[:fields]    = field_pos
  end

  tsv = TSV.open(StringIO.new(_get_file(organism, table, "txt")), options)
  tsv.key_field = key_field
  tsv.fields = fields
  tsv
end

.fields_for(organism, table) ⇒ Object 



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# File 'lib/rbbt/sources/ensembl_ftp.rb', line 93

def self.fields_for(organism, table)
  sql_file = _get_file(organism, File.basename(base_url(organism)), 'sql')
  chunk = sql_file.match(/^CREATE TABLE .#{table}. \((.*?)^\)/sm)[1]
  chunk.scan(/^\s+`(.*?)`/).flatten
end

.ftp_name_for(organism, subdir = 'mysql') ⇒ Object 



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# File 'lib/rbbt/sources/ensembl_ftp.rb', line 30

def self.ftp_name_for(organism, subdir='mysql')
  if domain = Thread.current["ensembl_domain"]
    return ftp_name_for_domain(domain, organism,subdir)
  end

  code, build = organism.split "/"
  build ||= "current"

  if build.to_s == "current"
    release = 'current'
    name = Organism.scientific_name(organism)
    ftp = Net::FTP.new(Ensembl::FTP::SERVER)
    ftp.passive = true
    ftp.
    dir = File.join('pub', "current_#{subdir}")
    ftp.chdir(dir)
    file = ftp.list(name.downcase.gsub(" ",'_') + "*").reject{|f| f.split("_").length > 3 && ! f.include?("_core_") }.collect{|l| l.split(" ").last}.last
    ftp.close
  else
    release = Ensembl.releases[build]
    name = Organism.scientific_name(organism)
    ftp = Net::FTP.new(Ensembl::FTP::SERVER)
    ftp.passive = true
    ftp.
    dir = File.join('pub', release, subdir)
    ftp.chdir(dir)
    file = ftp.list(name.downcase.gsub(" ",'_') + "*").reject{|f| f.split("_").length > 3 && ! f.include?("_core_") }.collect{|l| l.split(" ").last}.last
    ftp.close
  end
  [release, File.join(Ensembl::FTP::SERVER, dir, file)]
end

.ftp_name_for_domain(domain, organism, subdir = 'mysql') ⇒ Object 



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# File 'lib/rbbt/sources/ensembl_ftp.rb', line 14

def self.ftp_name_for_domain(domain, organism, subdir='mysql')
  code, build = organism.split "/"
  build ||= "current"

  release = build == "current" ? 'current' : Ensembl.releases[build]
  name = Organism.scientific_name(organism)
  ftp = Net::FTP.new(Ensembl::FTP::DOMAIN_SERVER)
  ftp.passive = true
  ftp.
  dir = File.join('pub', domain,  'current', subdir)
  ftp.chdir(dir)
  file = ftp.list(name.downcase.gsub(" ",'_') + "*").reject{|f|  f.split("_").length > 3 && ! f.include?("_core_") }.reject{|f| f =~ /\.gz$/}.collect{|l| l.split(" ").last}.last
  ftp.close
  [release, File.join(Ensembl::FTP::DOMAIN_SERVER, dir, file)]
end

.ftp_url_for(organism) ⇒ Object 



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# File 'lib/rbbt/sources/ensembl_ftp.rb', line 62

def self.ftp_url_for(organism)
  release, ftp_url = ftp_name_for(organism)
  ftp_url
end

.has_table?(organism, table) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/sources/ensembl_ftp.rb', line 88

def self.has_table?(organism, table)
  sql_file = _get_file(organism, File.basename(base_url(organism)), 'sql')
  ! sql_file.match(/^CREATE TABLE .#{table}. \((.*?)^\)/sm).nil?
end

.url_for(organism, table, extension) ⇒ Object 



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# File 'lib/rbbt/sources/ensembl_ftp.rb', line 71

def self.url_for(organism, table, extension)
  File.join(base_url(organism), table) + ".#{extension}.gz"
end