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rje_go V1.2

Gene Ontology Parsing/Manipulation Module

Module: rje_go
Description: Gene Ontology Parsing/Manipulation Module
Version: 1.2
Last Edit: 05/05/10

Copyright © 2008 Richard J. Edwards - See source code for GNU License Notice


Imported modules: rje rje_zen


See SLiMSuite Blog for further documentation. See rje for general commands.

Function

Parse the OBO V1.2 text download from GO into a data structure for querying by other programs, making GO Slims and mapping parent terms etc. Download input file from http://www.geneontology.org/GO.downloads.ontology.shtml. If no file is given, will attempt to download and parse http://www.geneontology.org/ontology/gene_ontology_edit.obo.

Commandline

obofile=FILE : Input GO OBO V1.2 download [None]
webobo=T/F : Whether to download from GO website if file not given [True]
goslim=LIST : List of GO IDs to form basis of GO Slim []
parentterms=LIST: Terms relating to parent relationships ['is_a','part_of']
ensgopath=PATH : Path to EnsGO files (!!! Restricted to Humans Currently !!!)

History Module Version History

    # 0.0 - Initial Compilation.
    # 1.0 - Working version with RJE modules. Added EnsGO Mapping from SLiMJIM.
    # 1.1 - Updated EnsGO mapping for new BioMart structure.
    # 1.2 - And again.

© 2015 RJ Edwards. Contact: richard.edwards@unsw.edu.au.