"""
def timenow():
"""return current time as a string
"""
return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
def rgConv(inpedfilepath,outhtmlname,outfilepath,plink):
"""
"""
basename = os.path.split(inpedfilepath)[-1] # get basename
outroot = os.path.join(outfilepath,basename)
cl = '%s --noweb --bfile %s --recode --out %s ' % (plink,inpedfilepath,outroot)
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
pbed_to_lped_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' % (myname,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()