opts, args = getopt.getopt(sys.argv[1:],'hr:i:o:H:',["filerank=","inputdir=","outputdir=","headers"])
except:
print help_message
sys.exit(2)
for opt, arg in opts:
if opt in ('-h','--help'):
print help_message
sys.exit()
elif opt in ('-r',"--filerank"):
fr = int(arg)-1
elif opt in ('-i','--inputdir'):
inputdir = arg
if inputdir[-1] != '/':
inputdir += '/'
elif opt in ('-o','--outputdir'):
outputdir = arg
if outputdir[-1] != '/':
outputdir += '/'
elif opt in ('-H',"--headers"):
headerdir = arg
if headerdir[-1] != '/':
headerdir += '/'
hashobject = Fastq_Reader(inputdir,outputdir)
FP = glob.glob(os.path.join(hashobject.input_path,'*.*'))
FP = list(set([fp[fp.rfind('/')+1:fp.rfind('.')] for fp in FP]))
file_group = FP[fr]
FP = glob.glob(os.path.join(headerdir,'*.hashq.*'))
originating_header = FP[int(file_group)]
originating_header = originating_header[originating_header.rfind('/')+1:originating_header.index('.hashq')]
hashobject.fastq_from_intermediate_output(file_group,originating_header)
