action='store_true',
default=False,
help="Add pseudocounts in the generated MM"
)
parser.add_argument('-k','--order',dest='order',action='store',type=int,
default=3,
help='It sets the order of the Markov Model used.')
args = parser.parse_args()
######## 1 TT SETS ######
training_filename='training_'+args.infile
testing_filename='testing_'+args.infile
m.training_testing_sets_separation(args.infile,3,training_filename,testing_filename)
######## 2 +/- ###########
(background, signal)=m.background_signal_separation(training_filename)
######## 3 kmer dict #####
if (args.pseudocounts):
back_dict=m.build_hash_pseudocount(background,args.order)
sign_dit=m.build_hash_pseudocount(signal,args.order)
else:
back_dict=m.build_hash(background,args.order)
sign_dit=m.build_hash(signal,args.order)
######### 4 print ########
m.print_hash(sign_dit,back_dict,args.outfile)
sys.exit()
m.training_testing_sets_separation(args.infile,3,training_filename,testing_filename)
######## 2 +/- ###########
######## 3 kmer dict #####
if (args.pseudocounts):
sys.stderr.write("Starting the training background and foreground separation...\n\n")
back_dict=m.build_hash_pseudocount([x for x in m.background_separation(training_filename)],args.order)
sys.stderr.write("The MM for the bg is generated...\n\n")
sign_dict=m.build_hash_pseudocount([x for x in m.signal_separation(training_filename)],args.order)
sys.stderr.write("The MM for the bg is generated...\n\n")
else:
back_dict=m.build_hash([x for x in m.background_separation(training_filename)],args.order)
sign_dict=m.build_hash([x for x in m.signal_separation(training_filename)],args.order)
######### 4 print ########
output_filename=args.outfile+'.MM'
sys.stderr.write("Printing the model in {}...\n\n".format(output_filename))
m.print_hash(sign_dict,back_dict,output_filename)
######## 5 windows #######
sys.stderr.write("Starting the testing background and foreground separation...\n\n")
sys.stderr.write("Starting the computation of the Scores...\n\n")
output_filename_fg=args.outfile+'_fg.th'
output_filename_bg=args.outfile+'_bg.th'
output_filename_all_top = args.outfile+'_all_top.th'
output_filename_all_bot = args.outfile+'_all_bot.th'
######## 0. ARG ########
parser = argparse.ArgumentParser(description='MMDI')
parser.add_argument('-i','--input',dest="infile", action="store", default= None,
help="Input Interval formated file")
parser.add_argument('-o','--MM_output', dest='outfile', action='store',
default=None,
help='The output file where the MM is going to be written.')
args = parser.parse_args()
######## 1 TT SETS ######
training_filename='training_'+args.infile
testing_filename='testing_'+args.infile
m.training_testing_sets_separation(args.infile,3,training_filename,testing_filename)
######## 2 +/- ###########
(background, signal)=m.background_signal_separation(training_filename)
######## 3 kmer dict #####
back_dict=m.build_hash(background,3)
sign_dit=m.build_hash(signal,3)
######### 4 print ########
m.print_hash(sign_dit,back_dict,args.outfile)
sys.exit()