--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rgenetics/rgGTOOL.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,58 @@
+#!/usr/local/bin/python
+# hack to run and process a linkage format file into
+# the format used by Marchini's SNPTEST imputed case control association
+# expects args as  
+#         rgGTOOL.py $i $o $discrete $logf $outdir
+# ross lazarus 
+
+import sys,math,shutil,subprocess,os,time
+from os.path import abspath
+imagedir = '/static/rg' # if needed for images
+myversion = 'V000.1 August 2007'
+
+def timenow():
+    """return current time as a string
+    """
+    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
+
+
+                
+if __name__ == "__main__":
+    if len(sys.argv) < 6:
+       s = 'rgGTOOL.py needs 5 params - got %s \n' % (sys.argv)
+       sys.stderr.write(s) # print >>,s would probably also work?
+       sys.exit(0)
+    print 'Rgenetics %s http://rgenetics.org SNPTEST Tools, rgGTOOL.py starting at %s' % (myversion,timenow())
+    pname = sys.argv[1]
+    lpedname = pname.split('.ped')[0] # get file name part
+    outname = sys.argv[2]
+    discrete = sys.argv[3]
+    logf = sys.argv[4]
+    outdir = sys.argv[5]
+    cdir = os.getcwd()
+    me = sys.argv[0]
+    mypath = abspath(os.path.join(cdir,me)) # get abs path to this python script
+    shpath = abspath(os.path.sep.join(mypath.split(os.path.sep)[:-1]))
+    alogf = abspath(os.path.join(cdir,logf)) # absolute paths
+    apedf = abspath(os.path.join(cdir,'%s.ped' % lpedname)) # absolute paths
+    amapf = abspath(os.path.join(cdir,'%s.map' % lpedname)) # absolute paths
+    outg = abspath(os.path.join(outdir,'%s.gen' % outname)) # absolute paths
+    outs = abspath(os.path.join(outdir,'%s.sample' % outname)) # absolute paths
+    workdir = abspath(os.path.sep.join(mypath.split(os.path.sep)[:-1])) # trim end off './database/files/foo.dat' 
+    os.chdir(workdir)
+    tlogname = '%s.logtemp' % outname
+    sto = file(tlogname,'w')
+    sto.write('rgGTOOL.py: called with %s\n' % (sys.argv)) 
+    exme = 'gtool'
+    vcl = [exme,'-P','--ped',apedf,'--map',amapf,'--discrete_phenotype',discrete,'--og',outg,'--os',outs]
+    #'/usr/local/bin/plink','/usr/local/bin/plink',pc1,pc2,pc3)
+    #os.spawnv(os.P_WAIT,plink,vcl)
+    p=subprocess.Popen(' '.join(vcl),shell=True,stdout=sto)
+    retval = p.wait()
+    sto.write('rgGTOOL.py after calling %s: vcl=%s\n' % (exme,vcl)) 
+    sto.close()
+    shutil.move(tlogname,alogf)
+    os.chdir(cdir)
+
+
+