A simple script to grab bioseqs by accession. Requires BioRuby. This just wraps the BioRuby fetch functionality in a friendly commandline interface. In brief, it can accept accession ids on the commandline or from a piped file (one accession per line) and save the corresponding sequences from the db. Sequences may be downloaded via the bioruby o…

fetch_seq_by_id.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