bartender_single_com

#!/usr/bin/python
import os
import sys
import getopt
import pdb
'''
print("Current path is ")
p = os.getcwd()
print p
sys.path.append(p)
'''
def usage():
	print "\tthere are 4 options, the first 2 is required, the remainings are optional,for help use -h or --help:"
	print " \t -f the input fastq file "
	print "\t -o the output prefix"
	print "\t -c the frequency cutoff. All clusters with size less then this threshold will not included in the result."
	print "\t -e the sequencing error. The default value is 0.01. Could be obtained by running the extraction components."
def driver():
	inputfile = ''
	outprefix = ''
	freq_cutoff = 1 
	error_rate = 0.01
    	try:
        	opt,args = getopt.getopt(sys.argv[1:],"f:o:c:e:h",["help"])
    	except getopt.error,msg:
		print("Invalid parameters!")
        	usage()
        	sys.exit(2)
    	for o,a in opt:
        	if o == '-f':
            		inputfile = a
            		if not os.path.isfile(inputfile):
                		print inputfile + " probably is not a valid file!\n"
                		sys.exit(2)
        	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 == '-e':
			try:
				error_rate = float(a)
				assert(error_rate <= 1)
				assert(error_rate >=0)
			except Exception as err:
				print("Invalid error rate specified!\n")
				sys.exit(2)
        	elif o in  ("-h","--help"):
            		print usage()
                	sys.exit(0)
	if not inputfile:
		print "There is no input sequence file specified"
		sys.exit(0)
	if not outprefix:
		print "There is no output file specified"
		sys.exit(0)
			
	os.system('bartender_single ' + inputfile + ' ' + outprefix + ' ' + str(freq_cutoff) + ' ' + str(error_rate))
if __name__=="__main__":
	print('Running bartender')
	driver()