Bio* Library for Clojure.

Biotools is my attempt at a basic bioinformatics file parsing library. You can find it over at GitHub. It can parse BLAST+ Tab output (-outfmt 6 std qlen slen), ExPASY ENZYME.dat, FASTA, GFF3, FPKM Tracking files from Cufflinks, Interproscan tab delimited output, Gene Ontology/Plant Ontology OBO format (any Ontology in OBO format), PMN Pathways format, ...

Reading genes.fpkm_tracking into Clojure/Incanter

I needed to analyze a large batch of samples (~300) of genes.fpkm_tracking files in Clojure and Incanter. This guide will show you how I read the files in, only looked at the FPKMs, and converted it into a single dataset. You need a project.clj file somewhere with the dependencies below (incanter, me.raynes.fs).

Experimenting with Pulsar in Clojure

I’ve now started using Pulsar instead of trying out core.async as I needed a lightweight barrier to entry. The problem: My database of choice (Neo4j) takes batch insertions in a single thread only, but clojure is by its very nature multi-threaded/concurrent/parallel (the exact wording of which I am no longer certain!). I process many files ...

Graph Database example using Gene Ontology – Part 1

Graph Database example using Gene Ontology - Part 1
The Gene Ontology project is a useful tool for anyone doing genomics. It’s a highly relational and controlled vocabulary, making it ideal for use in a graph database. In this example I will show you what a graph database is, and throughout this series we will create a graph database of GO terms, properly linked, ...