tallphil.co.uk

Sequences

Phil — Fri, 18 Nov 2011 17:10:43 +0000

A very common task for anyone involved in genetics is the manipulation of DNA or RNA sequences. I need to find the reverse compliment of sequences all the time, and I’ve been getting increasingly frustrated with the lack of a simple, robust tool to do that – most require strictly formatted sequences, use Java applets which take ages to load, and are generally faffy.

I thought I’d do something about this, so I made my own:
http://www.tallphil.co.uk/bioinformatics/sequences/

It does a couple of cool things, such as remembering your settings using HTML5 local storage, and giving the option to automatically copy results to the clipboard in internet explorer.

It’s free for anyone to use, and everything is included in the one HTML file. To host it on your own server just View Source, copy and paste..

[ Update : ] This project is now hosted on github – it’s still only one file (so you can still use or grab it by viewing source above), but github allows nice things like issue tracking, collaboration and forking…

-- Sequences tallphil.co.uk

Cambridge Kitchen Comments

Phil — Tue, 01 Nov 2011 17:28:35 +0000

My college, Trinity Hall, was recently in need of a new system to allow students and staff to comment on Hall food. As I couldn’t find anything that specifically met our need, I put together a standalone package. You can see a live demo (without Raven authentication) here.

It’s written in PHP and mySQL, and uses the excellent jQuery UI and jQuery Validate plugin.

Features:

Require Cambridge login using Raven
Comments require moderation

SCR, MCR and JCR each have their own moderators. These can be updated through the web interface.

Once moderated, kitchen staff are e-mailed about the comment, and can reply

Kitchen staff are also listed by CRSID and do not see commenting interface

Original commenter is e-mailed upon approval and reply
Users can also rate cafeteria food for quality and value using sliders
Moderators can delete comments, even after approval and reply
Users can delete their own comments, even after approval and reply
Optional lists of SCR, MCR and JCR members can be filled, and the system closed to anyone not on those lists.

These lists can also be updated through the web interface.

I have released the package with a GNU General Public License, meaning that anyone is free to use and modify the code as they need (though please leave the licence and credit in place). Cambridge colleges can easily use the system, hosted on the SRCF. Alternatively, you can download the comments package, and see a live demo (without Raven authentication) here.

-- Cambridge Kitchen Comments tallphil.co.uk

Genome RE Sites

Phil — Wed, 19 Oct 2011 14:50:44 +0000

Rather than sitting on my hard disk getting dusty, I thought I should start publishing the bioinformatics scripts that I’ve written over the past few years of my PhD.

The first to go up is a Perl script called “Genome RE Sites” – it searches a genome of your choice for a restriction endonuclease recognition site and outputs the co-ordinates of all cut sites.

[ Update ] : You can find an online version of this tool here.

I use a technique called Chromosome Conformation Capture, which uses restriction enzymes, so I frequently need to generate a list of cut sites to help me analyse data.

This script needs to be run on the command line, either on a linux system or using something like ActivePerl on Windows. Usage of this script is:

perl genome_RE_sites.pl [output file] [search string]

..where [output file] is the filename that will hold your results and [search string] is the restriction enzyme recognition site. The latter can be ignored and will default to HindIII (AAGCTT). There are a few other configuration options that you’ll need to edit before using the script, such as location of downloaded genome sequences and chromosome names. Please leave a comment if you have any problems with these.

Download the code here, or copy and paste from below:

#!/usr/bin/perl
use warnings;
use strict;
#############################################################
# Name: Genome RE Sites                                     #
# Author: Phil Ewels                                        #
# Version 1.0 - 25/05/2011                                  #
# --------------------------------------------------------- #
# Outputs a file with locations of restriction endonuclease #
# sites (not resulting fragments)                           #
# --------------------------------------------------------- #
# Genome RE Sites is licensed under a Creative Commons      #
# Attribution-ShareAlike 3.0 Unported License.              #
# Based on a work at www.tallphil.co.uk.                    #
#############################################################

#===============================
#==== CONFIGURATION OPTIONS ====
#===============================

# Set by command line (optional)
my ($output,$re_search) = @ARGV;
if (!defined $output) {
	die "Usage is genome_RE_sites.pl [output file] [search string]\nLeave blank to use defaults\n";
} elsif(!defined $re_search) {
	# Restriction site to use
	$re_search = 'AAGCTT'; # HindIII as default
	warn "Using file defaults: search string = $re_search, output = $output\n";
} else {
	warn "Using command line variables: search string = $re_search, output = $output\n";
}

# Path to chromosome fasta files. Replace chromosome number with %s
my $fn_base = 'D:\Genome Sequences\Mouse\chr%s.fa';
warn "Looking for Genome Sequences in $fn_base\n\n";

# Chromosomes to use. Default is (1..19,'X','Y') - other options are 'MT' etc.
my @chromosomes = (1..19,'X','Y');

#==================================
#== END OF CONFIGURATION OPTIONS ==
#==================================

open (OUT,'>',$output) or die $!;

# go through each chromosome
foreach my $chromosome (@chromosomes) {
	my $filename = sprintf($fn_base, $chromosome);
	open (IN,$filename) or die "Can't read file: $!";
	warn "Starting Chromosome $chromosome ($filename)\n";
	my $sequence = '';
	$_ = ; # Remove fasta header
	while (my $line = ) {
		chomp ($line);
		$sequence .= uc($line); # Make everything upper case
	}

	my $offset = 0;
	my $pos = index($sequence, $re_search, $offset);
	while ($pos != -1) {
		print OUT $chromosome."\t". # Chromosome Name
			      $pos."\t". # Position Start
			    ( $pos + length($re_search) )."\n"; # Position Finish
		$offset = $pos + length($re_search);
		$pos = index($sequence, $re_search, $offset);
	}

	close IN;
}

-- Genome RE Sites tallphil.co.uk

Taking WordPress Menus back to basics

Phil — Tue, 06 Sep 2011 16:43:43 +0000

I was working on a project earlier where I was using the wp_nav_menu function in WordPress to create a menu. By default, WordPress creates menus which are wrapped in layers (

), an unordered list (

) and then a link (). However, on this project I wanted to use jQuery UI to generate a navigation, and that required just links (
).

So, to strip out all of those extra HTML tags, I used the following javascipt (as I was already relying on jQuery and javascript anyway).
```
var newmenu = '';
jQuery("#nav ul li").each(function() {
	newmenu += jQuery(this).html();
});
jQuery("#nav").html(newmenu);
```
This works by firstly looping through all of the list items in my navigation layer, and copying their contents (the menu link) into a variable. Then, I replace all of the HTML contained within my navigation layer with that string. Easy!
-- Taking WordPress Menus back to basics tallphil.co.uk

Chosen jQuery Plugin

Phil — Thu, 28 Jul 2011 11:08:27 +0000

I just came across the Chosen JavaScript plugin, thanks to a link on the excellent CSS-Tricks RSS feed. It’s a jQuery / Prototype plugin which turns regular HTML