source: orange-bioinformatics/docs/reference-html/obiArrayExpress-test.py @ 1662:427f1876f3e6

Revision 1662:427f1876f3e6, 1.3 KB checked in by mitar, 2 years ago (diff)

Revamped documentation.

Line 
1import obiArrayExpress
2from pprint import pprint
3
4# test the gene_atlas_summary
5summary = obiArrayExpress.get_atlas_summary(["Kalrn", "Ptprd", "Mbp", "Cyfip2"], "Mus musculus")
6pprint(summary)
7
8# test query_atlas_simple
9results = obiArrayExpress.query_atlas_simple(genes=["Kalrn", "Ptprd", "Mbp", "Cyfip2"], organism="Mus musculus", regulation="up", condition="brain")
10pprint(results)
11
12# test Atlas Conditions
13gene_cond1 = obiArrayExpress.AtlasConditionGeneProperty("Goterm", "Is", "translation")
14gene_cond2 = obiArrayExpress.AtlasConditionGeneProperty("Disease", "Is", "cancer")
15org_cond = obiArrayExpress.AtlasConditionOrganism("Homo sapiens")
16
17conditions = obiArrayExpress.AtlasConditionList([gene_cond1, gene_cond2, org_cond])
18results = obiArrayExpress.query_atlas(conditions)
19pprint(results)
20
21# test ArrayExpress experiments, files query
22
23results = obiArrayExpress.query_experiments(accession="E-MEXP-31")
24pprint(results)
25
26results = obiArrayExpress.query_experiments(species="Homo sapines", expdesign="dose+response", ef="CellType")
27pprint(results)
28
29results = obiArrayExpress.query_experiments(species="Homo sapiens", gxa=True, assaycount=(1, 5), miamescore=(3, 5))
30pprint(results)
31
32results = obiArrayExpress.query_files(species="Mus musculus", gxa=True, keywords=["lung", "cancer"], miamescore=(3, 5), format="xml")
33print results
Note: See TracBrowser for help on using the repository browser.