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