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