R 2.12 to 2.13 package upgrade

If you:

• use Linux
• have just upgraded your R installation from 2.12 to 2.13
• installed some/all of your packages in your home area (e.g. ~/R/i486-pc-linux-gnu-library/2.12) and…
• …are wondering why R can’t see them any more

just do this:

# at a shell prompt
cp -r ~/R/i486-pc-linux-gnu-library/2.12 ~/R/i486-pc-linux-gnu-library/2.13
# in R console
update.packages(checkBuilt=TRUE, ask=FALSE)
# back to the shell
rm -rf ~/R/i486-pc-linux-gnu-library/2.12

update: corrected a typo; of course you need “cp -r”

Plotting “time of day” data using ggplot2

William asks:

How can I make a graph that looks like this, “tweet density” style, showing time intervals?

He then helpfully describes his input data: a CSV file with headers “time started, time finished, date”.

On parsing

Parsing – the act of ripping through a file, pulling out the relevant parts and doing something useful with them, is an integral part of bioinformatics. It can be a dull procedure. It can also be challenging, requiring creativity and imagination. Frequently as a bioinformatician, you will generate output from an unfamiliar program, or a colleague will bring you a file that you haven’t encountered. Your task is to figure out how the file is structured, which regular expressions are required to parse it, what kind of output to produce and most importantly, how to handle those rogue files which don’t obey the rules.

Here’s my top ten (language-agnostic) parsing tips, focusing only on non-XML text files.

Missing links: using SwissProt IDtracker in your code

The BioPerl Bio::DB::SwissProt module lets you fetch sequences from SwissProt by ID or AC and store them as sequence objects:

use Bio::DB::SwissProt;
my $sp = Bio::DB::SwissProt->new('-servertype' => 'expasy', 'hostlocation' => 'australia');
my $seq = $sp->get_Seq_by_id('myod1_pig');

If you obtained SwissProt identifiers from a database that hasn’t been updated for some time, you may find that the ID or AC has changed. For example at NLSdb, the ID from the example shown is given as “myod_pig”. In this case, BioPerl will throw an error like this:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: id does not exist
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::DB::WebDBSeqI::get_Seq_by_id /usr/local/share/perl/5.8.8/Bio/DB/WebDBSeqI.pm:154
STACK: test.pl:3
-----------------------------------------------------------

SwissProt provides a web page named IDtracker to help you find new identifiers using old ones. Here’s how we can integrate the service into Perl.

How to: map protein sequence onto chromosomal coordinates using BioPerl

My coding challenge this week: given a protein sequence and its exons, how do you map single amino acid residues to a location on a DNA sequence? It’s trickier than you might think. Read on for my latest BioPerl how-to.