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Tomaz Curk  committed 6f2b3c4

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Files changed (6)

File data/__init__.py

-#just a dummy package
-pass

File dist/GOLib-0.1.win32-py2.3.exe

Binary file removed.

File dist/GOLib-0.1.win32-py2.5.exe

Binary file removed.

File doc/golib.py

-import go
-go.loadAnnotation("sgd")
-go.loadGO()
-geneNames=[ "YBR085W", ## synonim for AAC3
-			"AAD10",
-			"21S_rRNA_4" ##synonim for 21S_RRNA
-			]
-uniqueGeneNames = [go.geneMapper[name] for name in geneNames]
-print uniqueGeneNames #should print ["AAC3", "AAD10", "21S_rRNA_4"]
-
-#finding all terms with the keywords "catabolic" and "process" in their names
-selectedTerms=filter(lambda term: "catabolic" in term.name and "process" in term.name, go.loadedGO.terms)
-for term in selectedTerms:
-	print term.id, term.name, term._def
-	
-def call(i): print i
-
-res=go.GOTermFinder(uniqueGeneNames, progressCallback=call)
-res=res.items()
-res.sort(lambda (_1,(_2,a,_3)), (_4,(_5,b,_6)): cmp(a,b))
-for GOId,(genes, p, n) in res:
-	print GOId, p, genes
-
-terms=go.GOTermFinder(uniqueGeneNames)
-terms=go.filterByPValue(terms, 0.2)
-go.drawEnrichmentGraph(terms, "enrichment_graph.png", width=600)

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File setup.py

-from distutils.core import setup, Extension
-
-module=Extension("_GOLib", sources=["go.c"])
-
-setup(name="GOLib",
-      version="0.1",
-      description="A library for handling gene ontologies",
-      author="Ales Erjavec",
-      author_email="ales.erjavec@fri.uni-lj.si",
-      ext_modules=[module],
-      py_modules=["go"],
-      packages=["data"],
-      extra_path="GOLib",
-      scripts=["post_install_script.py"]
-      )