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
matplotlib http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-1.0
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
1 maintainer
Metadata
1 maintainer
Release files for AIGO 0.1.0
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