21 lines
1.2 KiB
Markdown
21 lines
1.2 KiB
Markdown
---
|
|
author: einar
|
|
categories:
|
|
- General
|
|
- Linux
|
|
- Science
|
|
comments: true
|
|
date: "2006-11-25T09:06:10Z"
|
|
header:
|
|
image_fullwidth: banner_other.jpg
|
|
slug: a-simple-annotator
|
|
title: 'A simple annotator '
|
|
disable_share: true
|
|
wordpress_id: 132
|
|
---
|
|
|
|
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.
|