--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rgenetics/rgGLM_code.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,23 @@
+# before running the qc, need to rename various output files
+import os,string,time
+from galaxy import datatypes 
+
+
+def get_phecols(phef='',selectOne=0):
+   """return column names """
+   phepath = phef.extra_files_path
+   phename = phef.metadata.base_name
+   phe = os.path.join(phepath,'%s.pphe' % phename)
+   head = open(phe,'r').next()
+   c = head.strip().split()[2:] # first are fid,iid
+   res = [(cname,cname,False) for cname in c]
+   if len(res) >= 1:
+       if selectOne:
+          x,y,z = res[0] # 0,1 = fid,iid
+          res[0] = (x,y,True) # set second selected
+       else:
+          res.insert(0,('None','None',True))
+   else:
+      res = [('None','no phenotype columns found',False),]
+   return res
+