Post tagged: Bioruby

Coloring dendroscope files

How to programatically label phylogenies.

The need had arisen for the tips of a large phylogeny to be labelled in a systematic way. Rather than "point and click" within Dendroscope, this script takes a .den/dendro file and colors the tips according to a "color description" file. This is a simple csv file with taxa …

Consensus in BioRuby

Explaining the ill-explained ways to obtain a consensus sequence in BioRuby.

In BioRuby, alignments are equipped with several methods for obtaining consensus sequences. Unfortunately, these have terse descriptions which point you at the BioPerl documentation, with the added bonus of not quite working like the BioPerl equivalents.

First, let's create a very simple alignment, where everything agrees except the last sequence …

Reducing a sequence to SNPs

A script for a simple task.

A largely self-explanatory script. This will "shrink" an alignment, deleting all sites that don't contain a polymorphism in some member sequence. A little bit of script candy as well, this takes any number of files and saves the results in a new file named according to a definable schema:

#!/usr …

Fetch sequences from db

A simple script to grab bioseqs by accession.

This just wraps the BioRuby fetch functionality in a friendly commandline interface. In brief, it can accept accession ids on the commandline or from a piped file (one accession per line) and save the corresponding sequences from the db. Sequences may be downloaded via the bioruby or EBI servers. The …