Changeset 1707:7d692228fea1 in orange-bioinformatics for _bioinformatics/obiGeneSets.py


Ignore:
Timestamp:
08/13/12 16:05:04 (21 months ago)
Author:
markotoplak
Branch:
default
Message:

Speed up of setsig (obiGeneSetSig).

File:
1 edited

Legend:

Unmodified
Added
Removed
  • _bioinformatics/obiGeneSets.py

    r1643 r1707  
    77from __future__ import absolute_import, with_statement 
    88 
     9if __name__ == "__main__": 
     10    __package__ = "Orange.bio" 
     11 
    912import cPickle as pickle, os, tempfile, sys 
    1013from collections import defaultdict 
    1114 
    12 import orange 
     15import Orange.core as orange 
    1316from Orange.orng import orngServerFiles 
    1417 
     
    519522 
    520523if __name__ == "__main__": 
    521  
    522     #gs = keggGeneSets("9606") 
    523     akegg = collections((("KEGG",),"9606")) 
    524     a = collections({"PATH": ["g1","g2","g3"]}, "steroltalk.gmt", akegg) 
    525     for e in a: 
    526         print e 
    527     #print len(collections(keggGeneSets("9606"),(("KEGG",),"9606"), "C5.BP.gmt")) 
    528     #print len(collections((("KEGG",),"9606"), "C5.BP.gmt")) 
    529     #print sorted(list_all()) 
    530     #print len(collections((("KEGG",),"9606"), (("GO",), "9606"), "C5.BP.gmt")) 
    531     #register_local(keggGeneSets("9606")) 
    532     #register_local(goGeneSets("9606")) 
    533     #register_serverfiles(gs, rsf) 
    534     #print list_serverfiles_conn() 
    535     #print "Server list from index", list_serverfiles() 
    536524    rsf = orngServerFiles.ServerFiles(username=sys.argv[1], password=sys.argv[2]) 
    537525    upload_genesets(rsf) 
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