AIGO 0.1.0

Analysis and Inter-comparison of Gene Ontology functional annotations

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