andrewyatz’s gists

andrewyatz / gist:715849

Created November 25, 2010 20:09

Reallllyyy dumb way of doing secret santa

	public enum P {

	PERSON('[email protected]', true),
	OTHER('[email protected]', true),
	EH('[email protected]', true),

	private final String email
	private final Boolean satan

	private P(String email, Boolean satan) {

andrewyatz / SqlHelperBenchmark.pl

Created January 14, 2011 16:08

An attempt at showing what the impact of using callbacks are. In most versions of perl this is minimal

	use strict;
	use warnings;

	use Bio::EnsEMBL::Gene;
	use Bio::EnsEMBL::Registry;
	use Bio::EnsEMBL::Utils::SqlHelper;
	use Benchmark qw(cmpthese);

	Bio::EnsEMBL::Registry->load_registry_from_db(
	-HOST => 'mysql.ebi.ac.uk',

andrewyatz / storable_and_compress.pl

Created February 16, 2011 15:09

A way of plugging a storable call into a compress call & then ripping this back out @ the other end

	use strict;
	use warnings;

	use Data::Dumper; # Not required
	use Storable qw(nfreeze thaw);
	use IO::Compress::Gzip qw(gzip $GzipError); # qw() imports only for functional
	use IO::Uncompress::Gunzip qw(gunzip $GunzipError); # qw() imports only for functional

	#Just doing some quick obj hacks
	my $v = bless({ b => bless({ a => 1, c => [qw(x y z)]}, 'My::A') }, 'My::B');

andrewyatz / list_synteny.pl

Last active October 5, 2022 15:39

A way of printing synteny regions to screen or file from an ensembl or ensembl genomes resource

	#!/bin/env perl

	use strict;
	use warnings;

	use Getopt::Long;
	use Pod::Usage;
	use Bio::EnsEMBL::Registry;
	use Bio::EnsEMBL::Utils::Scalar qw(wrap_array);
	use IO::String;

andrewyatz / dicty_introns.pl

Created February 22, 2011 14:05

An Ensembl script for finding all the available introns for a single Gene for each of its transcripts & printing them to screen

	=head1 LICENSE

	Copyright (c) 1999-2011 The European Bioinformatics Institute and
	Genome Research Limited. All rights reserved.

	This software is distributed under a modified Apache license.
	For license details, please see

	http://www.ensembl.org/info/about/code_licence.html

andrewyatz / gist:849606

Created March 1, 2011 18:29

How to deadlock MySQL

	-- Setup the following schema
	CREATE TABLE `seq` (
	`id` int(11) unsigned NOT NULL AUTO_INCREMENT,
	`name` varchar(11) NOT NULL,
	`value` int(11) NOT NULL,
	PRIMARY KEY (`id`),
	UNIQUE KEY `name_idx` (`name`)
	) ENGINE=InnoDB;

andrewyatz / spawn_reap.pl

Created March 2, 2011 21:54

Spawning, selecting STDOUT/STDERR & reaping an external process in Perl

	use strict;
	use warnings;

	use IPC::Open3;
	use IO::Select;

	my $debug = 1;
	my $cmd = 'do something on the system';

	my ($in_fh, $out_fh, $err_fh);

andrewyatz / extracting_seqregions.pl

Created March 14, 2011 10:31

Code which looks for sequence regions in the Aedes database from Ensembl Metazoa

	use strict;
	use warnings;

	use Bio::EnsEMBL::Registry;

	Bio::EnsEMBL::Registry->load_registry_from_db(
	-host=>'mysql.ebi.ac.uk',
	-user=>'anonymous',
	-port=>4157,
	-db_version => 61

andrewyatz / eg_insdc_accessions.pl

Created March 28, 2011 10:15

Searching for an INSDC accession using the EBI Search for Ensembl Genomes species which have not had their contig level sequences mapped to an INSDC accession

	use strict;
	use warnings;

	use Bio::EnsEMBL::Registry;
	use SOAP::Lite;
	# Use the import below if you want to see more information from webservices
	# otherwise use the one above
	# use SOAP::Lite +trace => 'debug';

	my $species = 'aedes aegypti';

andrewyatz / downloading_dicty_introns.pl

Created April 5, 2011 09:22

An example script for downloading & storing introns from an Ensembl database (Dictyostelium discoideum)

	use strict;
	use warnings;
	use Bio::EnsEMBL::Registry;
	use Bio::EnsEMBL::DBSQL::DBConnection;
	use Bio::EnsEMBL::Utils::SqlHelper;

	#Load all DBs from Ensembl Genomes
	Bio::EnsEMBL::Registry->load_registry_from_db(
	-HOST => 'mysql.ebi.ac.uk',
	-PORT => 4157,

Andrew Yates andrewyatz