1000 genomes are making their genotypes available in variant call format (vcf). Now as others have noticed, vcf isn’t the prettiest format around. There are a few things to dislike:
The data is in ‘wide’ format which means that a file is fifteen screens wide and hides rare variation in a load of noise [...]
Categories: bioinformatics
I recently started using cogent – the COmparative GENomics Toolkit and discovered that it is an excellent piece of kit. A google search for ‘python ensembl‘ doesn’t even show it at all, yet it definitely has the best bindings for ensembl avaiable in python – they’re based on sqlalchemy making it easy enough to [...]
Categories: bioinformatics, ensembl, python
Python seems to have developed a decent set of tools for quickly building development environments. I want to store my notes on how to get a good environment for bioinformatics set up quickly.
First of all, if you haven’t already, install virtualenv and pip. Both are easy installable. Now install virtualenv wrapper.
Now we [...]
Categories: bioinformatics, python