Mercurial > repos > xuebing > sharplabtool

comparison tools/rgenetics/rgGLM_code.py @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1 # before running the qc, need to rename various output files
2 import os,string,time
3 from galaxy import datatypes
4
5
6 def get_phecols(phef='',selectOne=0):
7 """return column names """
8 phepath = phef.extra_files_path
9 phename = phef.metadata.base_name
10 phe = os.path.join(phepath,'%s.pphe' % phename)
11 head = open(phe,'r').next()
12 c = head.strip().split()[2:] # first are fid,iid
13 res = [(cname,cname,False) for cname in c]
14 if len(res) >= 1:
15 if selectOne:
16 x,y,z = res[0] # 0,1 = fid,iid
17 res[0] = (x,y,True) # set second selected
18 else:
19 res.insert(0,('None','None',True))
20 else:
21 res = [('None','no phenotype columns found',False),]
22 return res
23