|
0
|
1 #!/usr/local/bin/python
|
|
|
2 # hack to run and process a linkage format file into
|
|
|
3 # the format used by Marchini's SNPTEST imputed case control association
|
|
|
4 # expects args as
|
|
|
5 # rgGTOOL.py $i $o $discrete $logf $outdir
|
|
|
6 # ross lazarus
|
|
|
7
|
|
|
8 import sys,math,shutil,subprocess,os,time
|
|
|
9 from os.path import abspath
|
|
|
10 imagedir = '/static/rg' # if needed for images
|
|
|
11 myversion = 'V000.1 August 2007'
|
|
|
12
|
|
|
13 def timenow():
|
|
|
14 """return current time as a string
|
|
|
15 """
|
|
|
16 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
|
|
|
17
|
|
|
18
|
|
|
19
|
|
|
20 if __name__ == "__main__":
|
|
|
21 if len(sys.argv) < 6:
|
|
|
22 s = 'rgGTOOL.py needs 5 params - got %s \n' % (sys.argv)
|
|
|
23 sys.stderr.write(s) # print >>,s would probably also work?
|
|
|
24 sys.exit(0)
|
|
|
25 print 'Rgenetics %s http://rgenetics.org SNPTEST Tools, rgGTOOL.py starting at %s' % (myversion,timenow())
|
|
|
26 pname = sys.argv[1]
|
|
|
27 lpedname = pname.split('.ped')[0] # get file name part
|
|
|
28 outname = sys.argv[2]
|
|
|
29 discrete = sys.argv[3]
|
|
|
30 logf = sys.argv[4]
|
|
|
31 outdir = sys.argv[5]
|
|
|
32 cdir = os.getcwd()
|
|
|
33 me = sys.argv[0]
|
|
|
34 mypath = abspath(os.path.join(cdir,me)) # get abs path to this python script
|
|
|
35 shpath = abspath(os.path.sep.join(mypath.split(os.path.sep)[:-1]))
|
|
|
36 alogf = abspath(os.path.join(cdir,logf)) # absolute paths
|
|
|
37 apedf = abspath(os.path.join(cdir,'%s.ped' % lpedname)) # absolute paths
|
|
|
38 amapf = abspath(os.path.join(cdir,'%s.map' % lpedname)) # absolute paths
|
|
|
39 outg = abspath(os.path.join(outdir,'%s.gen' % outname)) # absolute paths
|
|
|
40 outs = abspath(os.path.join(outdir,'%s.sample' % outname)) # absolute paths
|
|
|
41 workdir = abspath(os.path.sep.join(mypath.split(os.path.sep)[:-1])) # trim end off './database/files/foo.dat'
|
|
|
42 os.chdir(workdir)
|
|
|
43 tlogname = '%s.logtemp' % outname
|
|
|
44 sto = file(tlogname,'w')
|
|
|
45 sto.write('rgGTOOL.py: called with %s\n' % (sys.argv))
|
|
|
46 exme = 'gtool'
|
|
|
47 vcl = [exme,'-P','--ped',apedf,'--map',amapf,'--discrete_phenotype',discrete,'--og',outg,'--os',outs]
|
|
|
48 #'/usr/local/bin/plink','/usr/local/bin/plink',pc1,pc2,pc3)
|
|
|
49 #os.spawnv(os.P_WAIT,plink,vcl)
|
|
|
50 p=subprocess.Popen(' '.join(vcl),shell=True,stdout=sto)
|
|
|
51 retval = p.wait()
|
|
|
52 sto.write('rgGTOOL.py after calling %s: vcl=%s\n' % (exme,vcl))
|
|
|
53 sto.close()
|
|
|
54 shutil.move(tlogname,alogf)
|
|
|
55 os.chdir(cdir)
|
|
|
56
|
|
|
57
|
|
|
58
|
