Changeset 1827:d9c6f60c5632 in orange-bioinformatics for _bioinformatics/obiGeneAtlasSets.py


Ignore:
Timestamp:
06/27/13 10:41:15 (10 months ago)
Author:
Flashpoint <vid.flashpoint@…>
Branch:
default
Message:

Removed the select/unselect all gene sets check box from OWSetEnrichment.py widget

File:
1 edited

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  • _bioinformatics/obiGeneAtlasSets.py

    r1826 r1827  
    44from Orange.bio.obiGeneAtlas import run_simple_query 
    55from Orange.bio.obiGeneSets import GeneSets, GeneSet 
     6import time 
    67 
    78def display_string(string): 
     
    1011regulation = "updown" 
    1112organism   = "Homo sapiens" 
    12 condition  = "cell_line" 
     13condition  = "organism_part" 
    1314org_code   = "9606" 
    1415max_pvalue = 1e-5 
     
    2728 
    2829for start in range(no_of_pages+1): 
     30    start = time.time() 
    2931    query = run_simple_query(regulation=regulation, organism=organism, condition=condition, start=start*no_of_genes, rows=no_of_genes) 
    3032    for result in query["results"]: 
    3133        i += 1 
    32         #print result["gene"]["name"] + "\t" + str(i) # For printing out gene names and the current number of genes during debugging 
     34        print result["gene"]["name"] + "\t" + str(i) # For printing out gene names and the current number of genes during debugging 
    3335        for exp in result["expressions"]:  
    3436            diff_exp = [e for e in exp["experiments"] if e["pvalue"] <= max_pvalue] # Use only genes that are significantly diff. expressed 
     
    3840                except: 
    3941                    sets[exp["efoTerm"], exp["efoId"]].append(result["gene"]["name"]) 
     42    print time.time() - start 
    4043         
    4144gene_sets = [] 
     
    5053final_set = GeneSets(gene_sets) 
    5154 
    52 #print final_set 
    53 #exit() 
     55print final_set 
     56exit() 
    5457 
    5558from Orange.bio.obiGeneSets import register 
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