"""
def timenow():
"""return current time as a string
"""
return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
def getMissval(inped=''):
"""
read some lines...ugly hack - try to guess missing value
should be N or 0 but might be . or -
"""
commonmissvals = {'N':'N','0':'0','n':'n','9':'9','-':'-','.':'.'}
try:
f = file(inped,'r')
except:
return None # signal no in file
missval = None
while missval == None: # doggedly continue until we solve the mystery
try:
l = f.readline()
except:
break
ll = l.split()[6:] # ignore pedigree stuff
for c in ll:
if commonmissvals.get(c,None):
missval = c
f.close()
return missval
if not missval:
missval = 'N' # punt
close(f)
return missval
def rgConv(inpedfilepath,outhtmlname,outfilepath,plink):
"""
"""
pedf = '%s.ped' % inpedfilepath
basename = os.path.split(inpedfilepath)[-1] # get basename
outroot = os.path.join(outfilepath,basename)
missval = getMissval(inped = pedf)
if not missval:
print '### lped_to_pbed_converter.py cannot identify missing value in %s' % pedf
missval = '0'
cl = '%s --noweb --file %s --make-bed --out %s --missing-genotype %s' % (plink,inpedfilepath,outroot,missval)
p = subprocess.Popen(cl,shell=True,cwd=outfilepath)
retval = p.wait() # run plink
def main():
"""
need to work with rgenetics composite datatypes
so in and out are html files with data in extrafiles path
lped_to_pbed_converter.py '$input1/$input1.metadata.base_name'
'$output1' '$output1.extra_files_path' '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink'
"""
nparm = 4
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]
outhtmlname = sys.argv[2]
outfilepath = sys.argv[3]
try:
os.makedirs(outfilepath)
except:
pass
plink = sys.argv[4]
rgConv(inpedfilepath,outhtmlname,outfilepath,plink)
f = file(outhtmlname,'w')
f.write(galhtmlprefix % prog)
flist = os.listdir(outfilepath)
s = '## Rgenetics: http://rgenetics.org Galaxy Tools %s %s' % (prog,timenow()) # becomes info
print s
f.write('
%s\n
' % (s))
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()