AIGO is a Python library for the Analysis and the Inter-comparison of Gene Ontology functional annotations. See (http://code.google.com/p/aigo).
Typical usage could look like this:
#!/usr/bin/env python
from AIGO.ReferenceSet import RefSet
from AIGO.FunctionalAnnotation import FuncAnnot
from AIGO.go.OBO import readGOoboXM
from AIGO.Analyse import AnalyseFA
from AIGO.Report import ReportFA
refSet = RefSet(organism="platipus", fileName="platipus.fasta", refType="Fasta")
G = readGOoboXML("go_daily-termdb.obo-xml", force=False)
FA = FuncAnnot("platipusProject", refSet, G, organism="platipus")
analyseFA = AnalyseFA()
analyseFA.largestSet([FA])
print("Largest sets of annotations:")
print("\t%d for %s" % (FA['largestSet']['All_aspects_of_GO'], FA.name))
analyseFA.coverage([FA])
analyseFA.obsolete([FA])
reportFA = ReportFA(outDir=None, name="platipusProject", organism="platipus")
reportFA.printStatistics([FA] ,["coverage", "obsolete"])
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Requirements:
· Python
· gtk+
· Biopython
· NumPy
· Matplotlib
· xlwt
· wxPython
· Psyco
· RPy
· PyGTK
· Pycairo
· pygobject
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