interPopula: a Python API to access the HapMap Project dataset

BMC Bioinformatics

Proceedings

Tiago Antao¹ 

[1] Liverpool School of Tropical Medicine, L3 5QA, Liverpool, UK;

关键词: Lactase;    HapMap Project;    HapMap Data;    HapMap Phase;    UCSC Genome Browser Database;   

DOI  :  10.1186/1471-2105-11-S12-S10

来源: Springer

【 摘 要 】

BackgroundThe HapMap project is a publicly available catalogue of common genetic variants that occur in humans, currently including several million SNPs across 1115 individuals spanning 11 different populations. This important database does not provide any programmatic access to the dataset, furthermore no standard relational database interface is provided.ResultsinterPopula is a Python API to access the HapMap dataset. interPopula provides integration facilities with both the Python ecology of software (e.g. Biopython and matplotlib) and other relevant human population datasets (e.g. Ensembl gene annotation and UCSC Known Genes). A set of guidelines and code examples to address possible inconsistencies across heterogeneous data sources is also provided.ConclusionsinterPopula is a straightforward and flexible Python API that facilitates the construction of scripts and applications that require access to the HapMap dataset.

【 授权许可】

CC BY   
© Antao; licensee BioMed Central Ltd. 2010