Changeset 208


Ignore:
Timestamp:
Sep 10, 2009, 9:31:04 AM (11 years ago)
Author:
marchulsman
Message:

Update omim-hugo-affy test

File:
1 edited

Legend:

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  • testhugo.py

    r4 r208  
    11from container import readfile,writefile
    22
    3 hugo_data = readfile('test/nomeids.txt',fieldnames="firstrow")
    4 omim_hugo = readfile('test/outOmimMiningHugo.txt',fieldnames=['id','cancer_type','hugo_symbol'])
    5 refseqids = (hugo_data *+ omim_hugo)[_.Symbol == _.hugo_symbol][_.cancer_type == "BREAST",7].fname('refseq_omim')
     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")
    67
    7 affy = readfile('test/annot_hgu133a.csv',sep=",",fieldnames="firstrow")
    8 affy2 = affy[:,[0,23]].fname('probeset_id','refseq_id')
    9 probeids = (refseqids *+ affy2)[_.refseq_omim == _.refseq_id].probeset_id
     8#couple data
     9omim_hugo_affy = omim.join(hugo,"hugo_symbol","Symbol").join(affy,"Refseq ID","refseq_id")
    1010
    11 writefile(probeids,'breast_omim.txt')
     11#filter on cancer type, select breast cancer probesets
     12bc_probeids = omim_hugo_affy[_.cancer_type == "BREAST"].probeset_id
     13
     14#write file with probeset ids
     15writefile(bc_probeids,'breastcancer_probesets.txt')
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