bartender_combiner_com

#!/usr/bin/env python
import os
import sys
import getopt

def usage():
    print("\tthere are 3 parameters and all are required. For help -h or -help")
    print("\t -c the cutoff that all clusters below this threshold will be removed from the result. ")
    print("\t -o the output prefix")
    print("\t -f the cluster results files from different time points. Only the cluster and quality files should be included. The files should be separated by comma")
def driver():
    inputfile = ''
    outprefix = ''
    freq_cutoff = 1 
    cluster_files = ''
    outprefix = ''
    try:
        opt,args = getopt.getopt(sys.argv[1:],"f:o:c:h",["help"])
    except getopt.GetoptError as msg:
        print(msg)
        usage()
        sys.exit(2)
    for o,a in opt:
        if o == '-f':
            inputfile = a.strip().split(',')
            if len(inputfile) % 2:
                print("The number of input files are not correct!")
                sys.exit(2)
            for f in inputfile:
                if not os.path.isfile(f):
                    print(f + " probably is not a valid file!\n")
                    sys.exit(2)
            inputfile = ' '.join(inputfile)
        elif o == '-o':
            outprefix = a 
            if not outprefix:
                print("No output file was specified!")
                sys.exit(2)
        elif o == '-c':
            try:
                freq_cutoff = int(a)
                assert(freq_cutoff > 0)
            except Exception as err:
                print("Frequency cutoff " + a + " is not a valid input!\n")
                sys.exit(2)
        elif o in  ("-h","--help"):
            print(usage())
            sys.exit(0)
    if not inputfile:
        print("There is no inputfile specified")
        print(usage())
        sys.exit(0)
    if not outprefix:
        print("There is no output file specified")
        print(usage())
        sys.exit(0)

    os.system('bartender_combiner ' + str(freq_cutoff) + ' ' + outprefix + ' ' + inputfile)
if __name__=="__main__":
    print('Running bartender_combiner')
    driver()