/tools/rgenetics/rgGTOOL.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 58 lines · 40 code · 8 blank · 10 comment · 2 complexity · 4d60178859b8cf76f16bdce4d35848f1 MD5 · raw file
- #!/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)