print errormessage
print "program terminated"
sys.exit(1)
maskinput =open('~maskedinput','w')
for id in index:
masked_seq = Pick70_mask.mask_longAT(seq_dic[id],"lower")
maskinput.write('>'+id+'\n')
maskinput.write(masked_seq+'\n')
maskinput.close()
os.environ['input'] = '~maskedinput'
fr, fw, fe = os.popen3('blastall -i "$input" -d $genome -a $cpunum -p blastn -v 50 -b 50 -e 1 -o ~tempblatout -F "m D" -U')
elif (VERSION =="BLAT"):
Pick70_mask.mask_file(tempinput,input+".mask","dust", "lower")
#blat version
fr,fw,fe = os.popen3('blat "$genome" "$input".mask -out=blast -qMask=lower ~tempblatout')
elif (VERSION =="GFCLIENT"):
Pick70_mask.mask_file(tempinput,input+".mask","dust", "lower")
#gfCleint version
fgfinfo = open(".gfServer_information",'r')
gfServer= string.strip(fgfinfo.read())
fgfinfo.close()
fieldnum = string.split(string.strip(gfServer))
if len(fieldnum) !=3:
print "Wrong Format of .gfServer_information file. It has only",fieldnum,"fields"
print "program terminated"
sys.exit(1)
os.environ['gfServer'] = gfServer
