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
