---
author: einar
comments: true
date: 2006-11-25 09:06:10+00:00
layout: post
slug: a-simple-annotator
title: 'A simple annotator '
wordpress_id: 132
categories:
- General
- Linux
- Science
---

In the past two days I've written a simple annotator program, that given an input list of RefSeq genes, automatically determines the relevant Entrez Gene IDs and annotates them using the flat files provided by the [NCBI](http://www.ncbi.nlm.nih.gov). A direct conversion was not possible due to limitations in Biopython's parsers, but I managed to use the GenBank parser to identify and extract the references to the Gene IDs (and putting them in a list).

Once that had been done, I created a series of dictionaries when reading the annotation file, for data such as gene name, symbol, chromosome and cytoband. Using the list I already obtained, it was easy to create a new file with the required fields.

During this process I learnt somewhat more about how to play with iterators to skip headings and so on. The code is not yet sufficiently generic, but once I finish toying with it, I may publish it for "general" (assuming anyone would use it) consumption, under GPL v2.
