"""
plinke = 'plink'
def timenow():
"""return current time as a string
"""
return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
def pruneLD(plinktasks=[],cd='./',vclbase = []):
"""
"""
fplog,plog = tempfile.mkstemp()
alog = []
alog.append('## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink pruneLD runner\n')
for task in plinktasks: # each is a list
vcl = vclbase + task
sto = file(plog,'w')
x = subprocess.Popen(' '.join(vcl),shell=True,stdout=sto,stderr=sto,cwd=cd)
retval = x.wait()
sto.close()
try:
lplog = file(plog,'r').readlines()
lplog = [x for x in lplog if x.find('Pruning SNP') == -1]
alog += lplog
alog.append('\n')
os.unlink(plog) # no longer needed
except:
alog.append('### %s Strange - no std out from plink when running command line\n%s\n' % (timenow(),' '.join(vcl)))
return alog
def makeLDreduced(basename,infpath=None,outfpath=None,plinke='plink',forcerebuild=False,returnFname=False,
winsize="60", winmove="40", r2thresh="0.1" ):
""" not there so make and leave in output dir for post job hook to copy back into input extra files path for next time
"""
ldr = basename # we store ld reduced and thinned data
ldreduced = os.path.join(outfpath,ldr) # note where this is going
outbase = os.path.join(outfpath,basename)
inbase = os.path.join(infpath)
loglines = []
ldbedname = '%s.bed' % ldreduced
bedname = '%s.bed' % basename
ldbedfn = os.path.join(infpath,ldbedname)
bedfn = os.path.join(infpath,bedname)
bmap = os.path.join(infpath,'%s.bim' % basename)
plinktasks = []
vclbase = [plinke,'--noweb']
plinktasks += [['--bfile',inbase,'--indep-pairwise %s %s %s' % (winsize,winmove,r2thresh),'--out %s' % outbase],
['--bfile',inbase,'--extract %s.prune.in --make-bed --out %s' % (outbase, outbase)]]
vclbase = [plinke,'--noweb']
loglines = pruneLD(plinktasks=plinktasks,cd=outfpath,vclbase = vclbase)
def main():
"""
need to work with rgenetics composite datatypes
so in and out are html files with data in extrafiles path
pbed_ldreduced_converter.py '$input1.extra_files_path/$input1.metadata.base_name' '$winsize' '$winmove' '$r2thresh'
'$output1' '$output1.files_path' 'plink'
"""
nparm = 7
if len(sys.argv) < nparm:
sys.stderr.write('## %s called with %s - needs %d parameters \n' % (prog,sys.argv,nparm))
sys.exit(1)
inpedfilepath = sys.argv[1]
base_name = os.path.split(inpedfilepath)[-1]
winsize = sys.argv[2]
winmove = sys.argv[3]
r2thresh = sys.argv[4]
outhtmlname = sys.argv[5]
outfilepath = sys.argv[6]
try:
os.makedirs(outfilepath)
except:
pass
plink = sys.argv[7]
makeLDreduced(base_name,infpath=inpedfilepath,outfpath=outfilepath,plinke=plink,forcerebuild=False,returnFname=False,
winsize=winsize,winmove=winmove,r2thresh=r2thresh)
f = file(outhtmlname,'w')
f.write(galhtmlprefix % prog)
flist = os.listdir(outfilepath)
s1 = '## Rgenetics: http://rgenetics.org Galaxy Tools %s %s' % (prog,timenow()) # becomes info
s2 = 'Input %s, winsize=%s, winmove=%s, r2thresh=%s' % (base_name,winsize,winmove,r2thresh)
print '%s %s' % (s1,s2)
f.write('
%s\n%s\n
' % (s1,s2))
for i, data in enumerate( flist ):
f.write('- %s
\n' % (os.path.split(data)[-1],os.path.split(data)[-1]))
f.write("
")
f.close()
if __name__ == "__main__":
main()