A simple script to download sequences by accession, vuia BioRuby. (Like much of BioRuby, finding a relevant example of how to do something can often be difficult.) It can accept accession ids on the commandline or by a piped file (one accession per line).

getseqbyid.rb

#!/usr/bin/env ruby
# download sequences from db by id

### IMPORTS

require 'bio'
require 'ostruct'
require 'timeout'
require 'pp'
require 'test/unit/assertions'

include Test::Unit::Assertions
include Test::Unit


### DEFINES & CONSTANTS

$SERVERS = {
    :bioruby => "http://bioruby.org/cgi-bin/biofetch.rb",
    :ebi => "http://www.ebi.ac.uk/cgi-bin/dbfetch",
}

$DEFAULTS = OpenStruct.new({
    :db => 'genbank',
    :overwrite => false,
    :read_stdin => false,
    :server => $SERVERS.keys[0]
})


### IMPLEMENTATION

def fetch_and_save_seq (fetch, db, id, overwrite)
    begin
        data = Bio::Fetch.query(db, id)
    
        filename = "#{id}.#{db}"
        assert(overwrite || (not File.exists?(filename)))
        File.open(filename, 'wb') { |f|
            f.write(data)
        }
        puts "'#{filename}' saved"

    rescue Timeout::Error => err
        puts "'#{id}' timed out, id possibly not in db"
    rescue AssertionFailedError => err
        puts "can't overwrite '#{filename}'"
    end

end


### MAIN

# Parse commandline arguments.
#
def parse_clargs(arg_arr)
   clopts = $DEFAULTS.dup()
   
   OptionParser.new { |opts|
      opts.program_name = __FILE__
      opts.banner = "Download sequences from online databases."
      opts.separator("")
      opts.separator("Reads sequence ids either from the commmandline or STDIN")
      opts.separator("and downloads them from the specified database.")
      opts.separator("")
      opts.separator("Usage: #{opts.program_name} [options] [ID1 ID2 ...]")
      
      opts.on('-h', '--help', 'Display this screen') {
         puts opts
         exit
      }
      
      opts.on('', '--server NAME', "Which server to query", $SERVERS.keys) { |v|
         clopts.servers = v
      }
            
      opts.on('', '--read-stdin', "Read sequence ids from standard input") {
         clopts.read_stdin = true
      }
      
      opts.on('-o', '--overwrite', "Overwrite pre-existing files") {
         clopts.overwrite = true
      }
      
      begin
         opts.parse!(arg_arr)
      rescue OptionParser::InvalidOption => e
         puts e
         puts opts
         exit 1
      end
   }
   
   pargs = arg_arr
   
   return clopts, pargs
end


def main
    clopts, pargs = parse_clargs(ARGV)
    
    url = $SERVERS[clopts.server]
    server = Bio::Fetch.new(url)
    db = clopts.db
    
    # handle positional arguments
    pargs.each { |e|
        fetch_and_save_seq(server, db, e, clopts.overwrite)
    }
    
    # parse stdin if asked to
    if clopts.read_stdin
        while (line = STDIN.gets())
            fetch_and_save_seq(server, db, line.strip(), clopts.overwrite)
        end
    end
    
end


if $0 == __FILE__
    main()
end


### END