source: testhugo.py

Last change on this file was 210, checked in by marchulsman, 10 years ago

Fix some bugs in qg_transform

File size: 608 bytes
Line 
1from container import readfile,writefile
2
3#read files
4omim = readfile('test/outOmimMiningHugo.txt', fieldnames=['id','cancer_type','hugo_symbol'])
5hugo = readfile('test/nomeids.txt', fieldnames="firstrow")
6affy = readfile('test/annot_hgu133a.csv', sep=",", fieldnames="firstrow")
7
8#couple data
9omim_hugo_affy = omim.join(hugo, "hugo_symbol", "Symbol").join(affy, "Ref Seq", "RefSeq Transcript ID")
10
11#filter on cancer type, select breast cancer probesets
12bc_probeids = omim_hugo_affy[_.cancer_type == "BREAST","Probe Set ID"]
13
14#write file with probeset ids
15writefile(bc_probeids,'breastcancer_probesets.txt')
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