wwood

#!/usr/bin/env perl

use lib '/home/ben/l/git/bioperl-live';

use 5.006;
use strict;
use warnings;
use Bio::Seq;
use Bio::SeqFeature::SubSeq;

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#!/usr/bin/env ruby
require 'bio-logger'


if __FILE__ == $0
  require 'optparse'
  # Parse cmd line options

  o = OptionParser.new do |opts|
    opts.banner = "gag [options] <pileup_output>"

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'escapenet': {
	name: 'EscapeNet',
	process: [
  'POST https://www.esc.net.au/myaccount/myaccount_login.php Action=Run&Redirect=%2Fmyaccount%2Fadsl%2Fadsl_usage.php&username={USERNAME}&password={PASSWORD}&submit=Log+In',
		[/Web access denied/, 'ERROR', /.*<td>([^<]+) \((\d+)Gb\).*\n.*usage is <\/td><td>(\d+) Mb of (\d+) Mb.*\n.*?Off-Peak Data<\/td><td>(\d+) Mb of (\d+) Mb.*\n.*?Rollover<\/td><td>(\d\d\/\d\d\/\d\d\d\d)/],

		'GET https://www.esc.net.au/myaccount/myaccount_logout.php',
	],

	varsDisplay: {

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sequenceserver/tests/database/nucleotide$ blast_formatter -version
blast_formatter: 2.2.25+
Package: blast 2.2.25, build Mar 21 2011 12:13:17
sequenceserver/tests/database/nucleotide$ ln -s Sinvicta2-2-3.cdna.subset.fasta parse.fa
sequenceserver/tests/database/nucleotide$ ln -s Sinvicta2-2-3.cdna.subset.fasta no_parse.fa
sequenceserver/tests/database/nucleotide$ makeblastdb -in parse.fa -parse_seqids -dbtype nucl


Building a new DB, current time: 09/25/2011 10:05:33
New DB name:   parse.fa

wwood

# This script is released under a GPL version 3 license or newer. Copyright by the author Ben Woodcroft.

require 'rubygems'
require 'ensembl'
require 'pp'

module Ensembl
  module Production
    class DBConnection < Ensembl::DBRegistry::Base
      self.abstract_class = true

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/* A mozilla Ubiquity helper to search for UniProt IDs */
CmdUtils.CreateCommand({
  names: ["uniprot"],
  icon: "http://www.uniprot.org/favicon.ico",
  description: "Searches UniProt.",
  help: "type 'uniprot something', enter. The something is like searching UniProt for an accession. For the format, add the format to the end of your accession - for instance 'uniprot C4IY21.txt'",
  author: { name: "Ben J. Woodcroft", email: "b.woodcroft near pgrad.unimelb.edu.au"},
  license: "GPL",
  arguments: [{role: 'object', nountype: noun_arb_text}],
  execute: function execute(args) {

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CmdUtils.CreateCommand({
  names: ["genbank blast"],
  arguments: [{role: 'object', nountype: noun_arb_text, label: 'genbank id'},
      {role: 'goal', nountype: noun_arb_text, label: 'blast database'},
      {role: 'instrument', nountype: noun_arb_text, label: 'blast program'},
      {role: 'location', nountype: noun_arb_text, label: 'taxa'}],
  homepage: "http://gist.github.com/73638",
  help: 'genbank_blast <b>entrez_id</b> [with <b>blast_program</b>] [to <b>blast_database_name</b>]',
  author: { name: "Ben J. Woodcroft", email: "b.woodcroft@pgrad.unimelb.edu.au"},
  contributors: ["Ben J. Woodcroft"],

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CmdUtils.CreateCommand({
  names: ["scholar"],
  icon: "http://www.google.com/favicon.ico",
  homepage: "http://static.isnotworking.com/scholar-search.html",
  description: "A short description of your command.",
  author: { name: "Ben Woodcroft", email: "b.woodcroft@pgrad.unimelb.edu.au"},
  license: "MPL",
  help: "Searches Google Scholar for articles",
  arguments: [{role:'object', nountype: noun_arb_text, label:'keywords'}],

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var ezp = 'http://ezp.lib.unimelb.edu.au/login?url=';

var link = FireGestures.getLinkURL();
var url = '';
var doc = FireGestures.sourceNode.ownerDocument;
if (!link){
  url = ezp+doc.location.href;
} else {
  url = link;
}

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A list of commands to install Ubiquity. All are compatible with Parser 2 (Ubiquity 0.5)

http://gist.github.com/180078 - google scholar 
http://gist.github.com/183528 - EuPathDB - PlasmoDB, ToxoDB.
http://gist.github.com/180067 - PubMed
http://gist.github.com/73638 - interacting with the Rails server I run locally
http://gist.github.com/168938 - Amigo Gene ontology searching
http://gist.github.com/168938 - Entrez commands
http://gist.github.com/270820 - Uniprot
http://gist.github.com/30649 - OrthoMCL