AIGO
HomePage: http://pypi.python.org/pypi/AIGO/
Author: Michael Defoin-Platel
Download: https://pypi.python.org/packages/source/A/AIGO/AIGO-0.1.0.tar.gz
=========== 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