Class: Bio::Fetch

Inherits:
Object show all
Defined in:
lib/bio/io/fetch.rb

Overview

DESCRIPTION

The Bio::Fetch class provides an interface to dbfetch servers. Given a database name and an accession number, these servers return the associated record. For example, for the embl database on the EBI, that would be a nucleic or amino acid sequence.

Possible dbfetch servers include:

If you’re behind a proxy server, be sure to set your HTTP_PROXY environment variable accordingly.

USAGE

require 'bio'

# Retrieve the sequence of accession number M33388 from the EMBL
# database.
server = Bio::Fetch.new()  #uses default server
puts server.fetch('embl','M33388')

# Do the same thing without creating a Bio::Fetch object. This method always
# uses the default dbfetch server: http://bioruby.org/cgi-bin/biofetch.rb
puts Bio::Fetch.query('embl','M33388')

# To know what databases are available on the bioruby dbfetch server:
server = Bio::Fetch.new()
puts server.databases

# Some databases provide their data in different formats (e.g. 'fasta',
# 'genbank' or 'embl'). To check which formats are supported by a given
# database:
puts server.formats('embl')

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(url = 'http://bioruby.org/cgi-bin/biofetch.rb') ⇒ Fetch

Create a new Bio::Fetch server object that can subsequently be queried using the Bio::Fetch#fetch method

Arguments:

Returns

Bio::Fetch object



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# File 'lib/bio/io/fetch.rb', line 74

def initialize(url = 'http://bioruby.org/cgi-bin/biofetch.rb')
  @url = url
  schema, user, @host, @port, reg, @path, = URI.split(@url)
end

Instance Attribute Details

#database ⇒ Object

The default database to query – This will be used by the get_by_id method ++



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# File 'lib/bio/io/fetch.rb', line 83

def database
  @database
end

Class Method Details

.query(*args) ⇒ Object

Shortcut for using BioRuby’s BioFetch server. You can fetch an entry without creating an instance of BioFetch server. This method uses the default dbfetch server, which is bioruby.org/cgi-bin/biofetch.rb

Example:

puts Bio::Fetch.query('refseq','NM_12345')

Arguments:

  • database: name of database to query (see Bio::Fetch#databases to get list of supported databases)

  • id: single ID or ID list separated by commas or white space

  • style: [raw|html] (default = ‘raw’)

  • format: name of output format (see Bio::Fetch#formats)



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# File 'lib/bio/io/fetch.rb', line 125

def self.query(*args)
  self.new.fetch(*args)
end

Instance Method Details

#databases ⇒ Object

Using this method, the user can ask a dbfetch server what databases it supports. This would normally be the first step you’d take when you use a dbfetch server for the first time. Example:

server = Bio::Fetch.new()
puts server.databases # returns "aa aax bl cpd dgenes dr ec eg emb ..."

This method only works for the bioruby dbfetch server. For a list of databases available from the EBI, see the EBI website at www.ebi.ac.uk/cgi-bin/dbfetch/

Returns

array of database names



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# File 'lib/bio/io/fetch.rb', line 141

def databases
  query = "info=dbs"

  Bio::Command.read_uri(@url + '?' + URI.escape(query)).strip.split(/\s+/)
end

#fetch(db, id, style = 'raw', format = nil) ⇒ Object

Fetch a database entry as specified by database (db), entry id (id), ‘raw’ text or ‘html’ (style), and format. When using BioRuby’s BioFetch server, value for the format should not be set. Examples:

server = Bio::Fetch.new('http://www.ebi.ac.uk/cgi-bin/dbfetch')
puts server.fetch('embl','M33388','raw','fasta')
puts server.fetch('refseq','NM_12345','html','embl')

Arguments:

  • database: name of database to query (see Bio::Fetch#databases to get list of supported databases)

  • id: single ID or ID list separated by commas or white space

  • style: [raw|html] (default = ‘raw’)

  • format: name of output format (see Bio::Fetch#formats)



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# File 'lib/bio/io/fetch.rb', line 104

def fetch(db, id, style = 'raw', format = nil)
  query = [ "db=#{db}", "id=#{id}", "style=#{style}" ]
  query.push("format=#{format}") if format
  query = query.join('&')
  
  Bio::Command.read_uri(@url + '?' + URI.escape(query))
end

#formats(database = @database) ⇒ Object

Lists the formats that are available for a given database. Like the Bio::Fetch#databases method, this method is only available on the bioruby dbfetch server. Example:

server = Bio::Fetch.new()
puts server.formats('embl') # returns "default fasta"

Arguments:

  • database

    name of database you want the supported formats for

Returns

array of formats



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# File 'lib/bio/io/fetch.rb', line 157

def formats(database = @database)
  if database
    query = "info=formats;db=#{database}"

    Bio::Command.read_uri(@url + '?' + URI.escape(query)).strip.split(/\s+/)
  end
end

#get_by_id(id) ⇒ Object

Get raw database entry by id. This method lets the Bio::Registry class use Bio::Fetch objects.



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# File 'lib/bio/io/fetch.rb', line 87

def get_by_id(id)
  fetch(@database, id)
end

#maxids ⇒ Object

A dbfetch server will only return entries up to a given maximum number. This method retrieves that number from the server. As for the databases and formats methods, the maxids method only works for the bioruby dbfetch server.

Arguments: none

Returns

number



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# File 'lib/bio/io/fetch.rb', line 172

def maxids
  query = "info=maxids"

  Bio::Command.read_uri(@url + '?' + URI.escape(query)).to_i
end