andrewyatz’s gists

andrewyatz / ucsc_binary_downloader.pl

Created April 13, 2011 15:50

A script which downloads all x86_64 binaries from UCSC's download server. You can invoke it like ./ucsc_binary_downloader.pl or ./ucsc_binary_downloader.pl blat. The first version will download everything in the root dir or linux.x86_64 and the second wil

	#!/usr/bin/env perl

	use strict;
	use warnings;
	use WWW::Mechanize;
	use LWP::Simple;

	my $href = 'http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/';

	if($ARGV[0]) {

andrewyatz / synteny_to_psl.pl

Created May 3, 2011 08:38

A script for extracting synteny regions from Ensembl & Ensembl Genomes databases into PSL (UCSC/Blat alignment report format).

	#!/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 / funky_db_work_with_ensembl.pl

Created May 24, 2011 20:30

Example of connecting to an Ensembl database using a registry, getting said species & running SQL done 4 ways

	use strict;
	use warnings;

	use Bio::EnsEMBL::Registry;
	use Bio::EnsEMBL::Utils::SqlHelper;

	#Set to the registry location
	my $registry_location = $ARGV[0];
	#Set this to the target species e.g. e_coli_k12
	my $species = $ARGV[1];

andrewyatz / dump_every_genetree.pl

Created June 7, 2011 15:52

Two ways of getting alignments of clusters from a compara database and writing these out to a file.

	use strict;
	use warnings;
	use Bio::EnsEMBL::Registry;
	use Bio::AlignIO;

	Bio::EnsEMBL::Registry->load_registry_from_db(
	-HOST => 'mysql.ebi.ac.uk',
	-PORT => 4157,
	-USER => 'anonymous',
	-DB_VERSION => 62

andrewyatz / phyloxml_to_fasta.pl

Created June 7, 2011 16:41

Converting a PhyloXML file to a FASTA alignment

	#Only supports a PhyloXML file with only one phylogeny element. This is intended as an extension point

	use strict;
	use warnings;
	use XML::Twig;

	my $file = '/Users/ayates/Desktop/tmp.xml';

	my $id;
	my $seqs = [];

andrewyatz / phyloxml_to_msa.pl

Created June 8, 2011 09:44

Convert a PhyloXML file to any BioPerl supported alignment format

	#!/bin/env perl

	use strict;
	use warnings;

	use Bio::AlignIO;
	use Bio::LocatableSeq;
	use Bio::SimpleAlign;
	use IO::Handle;
	use IO::File;

andrewyatz / dump_homology_tsv.pl

Created June 8, 2011 16:14

Script used to dump homology information into a tabbed separated value file

	#!/bin/env perl

	use strict;
	use warnings;

	use Bio::EnsEMBL::ApiVersion;
	use Bio::EnsEMBL::Utils::SqlHelper;
	use Bio::EnsEMBL::Registry;
	use File::Spec;
	use Getopt::Long;

andrewyatz / dump_xrefs_tsv.pl

Created June 9, 2011 12:01

Retrieve an Xref mapping file from any Ensembl based database

	#!/bin/env perl

	use strict;
	use warnings;

	use Bio::EnsEMBL::ApiVersion;
	use Bio::EnsEMBL::Utils::SqlHelper;
	use Bio::EnsEMBL::Registry;
	use File::Spec;
	use Getopt::Long;

andrewyatz / setting_up_a_new_remote_git_repository.textile

Created June 21, 2011 08:54 — forked from toolmantim/setting_up_a_new_remote_git_repository.textile

(a gist based on the old toolmantim article on setting up remote repos)

To collaborate in a distributed development process you’ll need to push code to remotely accessible repositories.

This is somewhat of a follow-up to the previous article setting up a new rails app with git.

For the impatient

Set up the new bare repo on the server:

andrewyatz / find_upi.groovy

Created July 20, 2011 11:05

Uses the UniProtJAPI and BioJava3 to process a FASTA file and then outputs the appropriate UPI.


	#!/usr/bin/env groovy

	@GrabResolver(name='ebi', root='http://www.ebi.ac.uk/~maven/m2repo')
	@Grab(group='uk.ac.ebi.uniprot.kraken', module='uniprotjapi', version='2011.07')
	@Grab(group='org.biojava', module='biojava3-core', version='3.0')
	@Grab(group='com.google.code.gson', module='gson', version='1.7.1')

	import org.biojava3.core.sequence.io.FastaReaderHelper
	import org.biojava3.core.sequence.template.SequenceMixin

Andrew Yates andrewyatz

For the impatient