Changeset 209


Ignore:
Timestamp:
Sep 10, 2009, 4:37:04 PM (11 years ago)
Author:
marchulsman
Message:

More changes to testhugo.py

File:
1 edited

Legend:

Unmodified
Added
Removed
  • testhugo.py

    r208 r209  
    22
    33#read files
    4 omim = readfile('test/outOmimMiningHugo.txt',fieldnames=['id','cancer_type','hugo_symbol'])
    5 hugo = readfile('test/nomeids.txt',fieldnames="firstrow")
    6 affy = readfile('test/annot_hgu133a.csv',sep=",",fieldnames="firstrow")
     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")
    77
    88#couple data
    9 omim_hugo_affy = omim.join(hugo,"hugo_symbol","Symbol").join(affy,"Refseq ID","refseq_id")
     9omim_hugo_affy = omim.join(hugo, "hugo_symbol", "Symbol").join(affy, "Ref Seq", "RefSeq Protein ID")
    1010
    1111#filter on cancer type, select breast cancer probesets
    12 bc_probeids = omim_hugo_affy[_.cancer_type == "BREAST"].probeset_id
     12bc_probeids = omim_hugo_affy[_.cancer_type == "BREAST","Probe Set ID"]
    1313
    1414#write file with probeset ids
Note: See TracChangeset for help on using the changeset viewer.