"""
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):
"""convert linkage ped/map to fbat"""
recode={'A':'1','C':'2','G':'3','T':'4','N':'0','0':'0','1':'1','2':'2','3':'3','4':'4'}
basename = os.path.split(inpedfilepath)[-1] # get basename
inmap = '%s.map' % inpedfilepath
inped = '%s.ped' % inpedfilepath
outf = '%s.ped' % basename # note the fbat exe insists that this is the extension for the ped data
outfpath = os.path.join(outfilepath,outf) # where to write the fbat format file to
try:
mf = file(inmap,'r')
except:
sys.stderr.write('%s cannot open inmap file %s - do you have permission?\n' % (prog,inmap))
sys.exit(1)
try:
rsl = [x.split()[1] for x in mf]
except:
sys.stderr.write('## cannot parse %s' % inmap)
sys.exit(1)
try:
os.makedirs(outfilepath)
except:
pass # already exists
head = ' '.join(rsl) # list of rs numbers
# TODO add anno to rs but fbat will prolly barf?
pedf = file(inped,'r')
o = file(outfpath,'w',2**20)
o.write(head)
o.write('\n')
for i,row in enumerate(pedf):
if i == 0:
lrow = row.split()
try:
x = [int(x) for x in lrow[10:50]] # look for non numeric codes
except:
dorecode = 1
if dorecode:
lrow = row.strip().split()
p = lrow[:6]
g = lrow[6:]
gc = [recode.get(x,'0') for x in g]
lrow = p+gc
row = '%s\n' % ' '.join(lrow)
o.write(row)
o.close()
def main():
"""call fbater
need to work with rgenetics composite datatypes
so in and out are html files with data in extrafiles path
rg_convert_lped_fped.py '$input1/$input1.metadata.base_name'
'$output1' '$output1.extra_files_path'
"""
nparm = 3
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
rgConv(inpedfilepath,outhtmlname,outfilepath)
f = file(outhtmlname,'w')
f.write(galhtmlprefix % prog)
flist = os.listdir(outfilepath)
print '## Rgenetics: http://rgenetics.org Galaxy Tools %s %s' % (prog,timenow()) # becomes info
f.write('
## Rgenetics: http://rgenetics.org Galaxy Tools %s %s\n
' % (prog,timenow()))
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()