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#
# = bio/io/biofetch.rb - BioFetch access module
#
# Copyright:: Copyright (C) 2002, 2005 Toshiaki Katayama <k@bioruby.org>,
# Copyright (C) 2006 Jan Aerts <jan.aerts@bbsrc.ac.uk>
# License:: The Ruby License
#
# == DESCRIPTION
#
# Using EBI Dbfetch server
#
# ebi_server = Bio::Fetch::EBI.new
# puts ebi_server.fetch('embl', 'J00231')
# puts ebi_server.fetch('embl', 'J00231', 'raw')
# puts ebi_server.fetch('embl', 'J00231', 'html')
#
# Getting metadata from EBI Dbfetch server
#
# puts ebi_server.databases
# puts ebi_server.formats('embl')
# puts ebi_server.maxids
#
# Using EBI Dbfetch server without creating a Bio::Fetch::EBI instance
#
# puts Bio::Fetch::EBI.query('ena_sequence', 'J00231')
# puts Bio::Fetch::EBI.query('ena_sequence', 'J00231', 'raw', 'fasta')
#
# Using a BioFetch server with specifying URL
#
# server = Bio::Fetch.new('http://www.ebi.ac.uk/Tools/dbfetch/dbfetch')
# puts server.fetch('ena_sequence', 'J00231')
# puts server.fetch('ena_sequence', 'J00231', 'raw', 'fasta')
#
require 'uri'
require 'cgi'
require 'bio/command'
module Bio
# = 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:
# * http://www.ebi.ac.uk/Tools/dbfetch/dbfetch
#
# Note that old URL http://www.ebi.ac.uk/cgi-bin/dbfetch still alives
# probably because of compatibility, but using the new URL is recommended.
#
# Historically, there were other dbfetch servers including:
# * http://bioruby.org/cgi-bin/biofetch.rb (default before BioRuby 1.4)
# But they are unavailable now.
#
#
# 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::EBI.new #uses EBI server
# puts server.fetch('ena_sequence','M33388')
#
# # database name "embl" can also be used though it is not officially listed
# puts server.fetch('embl','M33388')
#
# # Do the same thing with explicitly giving the URL.
# server = Bio::Fetch.new(Bio::Fetch::EBI::URL) #uses EBI server
# puts server.fetch('ena_sequence','M33388')
#
# # Do the same thing without creating a Bio::Fetch::EBI object.
# puts Bio::Fetch::EBI.query('ena_sequence','M33388')
#
# # To know what databases are available on the dbfetch server:
# server = Bio::Fetch::EBI.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')
#
class Fetch
# Bio::Fetch::EBI is a client of EBI Dbfetch
# (http://www.ebi.ac.uk/Tools/dbfetch/dbfetch).
#
# An instance of this class works the same as:
# obj = Bio::Fetch.new("http://www.ebi.ac.uk/Tools/dbfetch/dbfetch")
# obj.database = "ena_sequence"
#
# See the documents of Bio::Fetch for more details.
class EBI < Fetch
# EBI Dbfetch server URL
URL = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch".freeze
# For the usage, see the document of Bio::Fetch.new.
def initialize(url = URL)
@database = "ena_sequence"
super
end
# Shortcut for using EBI Dbfetch server. You can fetch an entry
# without creating an instance of Bio::Fetch::EBI. This method uses
# EBI Dbfetch server http://www.ebi.ac.uk/Tools/dbfetch/dbfetch .
#
# Example:
# puts Bio::Fetch::EBI.query('refseq','NM_123456')
# puts Bio::Fetch::EBI.query('ena_sequence','J00231')
#
# ---
# *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)
def self.query(*args)
self.new.fetch(*args)
end
end #class EBI
# Create a new Bio::Fetch server object that can subsequently be queried
# using the Bio::Fetch#fetch method.
#
# You must specify _url_ of a server.
# The preset default server is deprecated.
#
# If you want to use a server without explicitly specifying the URL,
# use Bio::Fetch::EBI.new that uses EBI Dbfetch server.
#
# ---
# *Arguments*:
# * _url_: URL of dbfetch server. (no default value)
# *Returns*:: Bio::Fetch object
def initialize(url = nil)
unless url then
raise ArgumentError, "No server URL is given in Bio::Fetch.new. The default server URL value have been deprecated. You must explicitly specify the url or use Bio::Fetch::EBI for using EBI Dbfetch."
end
@url = url
end
# The default database to query
#--
# This will be used by the get_by_id method
#++
attr_accessor :database
# Get raw database entry by id. This method lets the Bio::Registry class
# use Bio::Fetch objects.
def get_by_id(id)
fetch(@database, id)
end
# Fetch a database entry as specified by database (db), entry id (id),
# 'raw' text or 'html' (style), and format.
#
# 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)
def fetch(db, id, style = 'raw', format = nil)
query = [ [ 'db', db ],
[ 'id', id ],
[ 'style', style ] ]
query.push([ 'format', format ]) if format
_get(query)
end
# 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 works for EBI Dbfetch server (and for the bioruby dbfetch
# server). Not all servers support this method.
# ---
# *Returns*:: array of database names
def databases
_get_single('info', 'dbs').strip.split(/\s+/)
end
# Lists the formats that are available for a given database. Like the
# Bio::Fetch#databases method, not all servers support this method.
# This method is available on the EBI Dbfetch server (and on the bioruby
# dbfetch server).
#
# Example:
# server = Bio::Fetch::EBI.new()
# puts server.formats('embl') # returns [ "default", "annot", ... ]
# ---
# *Arguments*:
# * _database_:: name of database you want the supported formats for
# *Returns*:: array of formats
def formats(database = @database)
if database
query = [ [ 'info', 'formats' ],
[ 'db', database ] ]
_get(query).strip.split(/\s+/)
end
end
# 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, not all servers support the maxids method.
# This method is available on the EBI Dbfetch server (and on the bioruby
# dbfetch server).
#
# Example:
# server = Bio::Fetch::EBI.new
# puts server.maxids # currently returns 200
# ---
# *Arguments*: none
# *Returns*:: number
def maxids
_get_single('info', 'maxids').to_i
end
private
# (private) query to the server.
# ary must be nested array, e.g. [ [ key0, val0 ], [ key1, val1 ], ... ]
def _get(ary)
query = ary.collect do |a|
"#{CGI.escape(a[0])}=#{CGI.escape(a[1])}"
end.join('&')
Bio::Command.read_uri(@url + '?' + query)
end
# (private) query with single parameter
def _get_single(key, val)
query = "#{CGI.escape(key)}=#{CGI.escape(val)}"
Bio::Command.read_uri(@url + '?' + query)
end
end
end # module Bio
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