Metadata-Version: 1.0
Name: AIGO
Version: 0.1.0
Summary: Analysis and Inter-comparison of Gene Ontology functional annotations
Home-page: http://pypi.python.org/pypi/AIGO/
Author: Michael Defoin-Platel
Author-email: michael.defoinplatel@gmail.com
License: LICENSE.txt
Description: ===========
           AIGO
        ===========
        
        AIGO is a python library for the Analysis and 
        the Inter-comparison of Gene Ontology functional annotations.
        see (http://code.google.com/p/aigo).
        
        Created by Michael Defoin-Platel on 21/02/2010.
        Copyright (c) 2010. All rights reserved.
        
        Typical usage could look like this::
        
            #!/usr/bin/env python
        
            from AIGO import logger
        
            from AIGO.ReferenceSet import RefSet
            from AIGO.FunctionalAnnotation import FuncAnnot
            from AIGO.go.OBO import readGOoboXML
        
            from AIGO.Analyse import AnalyseFA
            from AIGO.Report import ReportFA
        
            from AIGO.utils.Execute import batchExecute
        
            refSet = RefSet(organism="platypus", fileName="platypus.refSet", refType="Text")
            G = readGOoboXML("go_daily-termdb.obo-xml")
            FA = FuncAnnot("platypusProject", refSet, G, organism="platypus")
            FA.read("platypus.gaf", "GAF") 
        
            analyseFA = AnalyseFA()
        
            analyseFA.largestSet([FA])
            logger.info("Largest sets of annotations:")
            logger.info("\t%d for %s" % (FA['largestSet']['All_aspects_of_GO'], FA.name))
        
            batchList=["coverage",  "richness", "numberAnnot", "redundancy", "specificity", "informationContent"]
            batchExecute(batchList, analyseFA, [FA])
        
            reportFA = ReportFA(outDir=None, name="platypusProject", organism="platypus")
            reportFA.printStatistics([FA] ,batchList)
        
        Tests
        =====
        
        Run testAIGO.py in the tests directory
        
        
        Requirements
        ==============
        
        Running AIGO on windows
        -------------------------
        * The 2.6.5 Python interpreter for Windows page http://www.python.org/download.
        * GTK+ runtime (recommend bundle), PyGTK, PyCairo? and PyGObject http://www.pygtk.org/downloads.html
        * BioPython? http://biopython.org/wiki/Download
        * NumPy? http://sourceforge.net/projects/numpy/files/NumPy
        * matplotlib http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-1.0
        * xlwt http://pypi.python.org/pypi/xlwt 
        
        Optional :
        * wxPython http://www.wxpython.org/download.php#binaries
        * psyco http://sourceforge.net/projects/psyco/files
        * RPy http://sourceforge.net/projects/rpy/files
        
        
        Contributors
        ============
        * Michael Defoin-Platel
        * Matthew Hindle
        
Platform: UNKNOWN
