def main(argv):
inputfile = ''
file_name = ''
k_mer_arg=''
default_file_name='input_DNA.txt'
k_mer_ln=10 #default value for the length of the pattern
try:
opts, args = getopt.getopt(argv,"hi:k:")
except getopt.GetoptError:
print 'Usage: '+os.path.basename(__file__)+ ' -i <inputfile> -k <k-mer length>'
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print 'Usage: '+os.path.basename(__file__)+ ' -i <inputfile> -k <k-mer length>'
sys.exit()
elif opt in ("-i"):
inputfile = arg
elif opt in ("-k"):
k_mer_arg = arg
if (len(inputfile))>0:
file_name=inputfile
print 'Using DNA inputfile: '+inputfile
else:
file_name=default_file_name
print 'Using default inputfile: '+file_name
try:
int(k_mer_arg)>0
k_mer_ln=int(k_mer_arg)
print 'Length of k-mer is '+ str(k_mer_ln)+' bp'
except:
print 'Using default k-mer length of '+str(k_mer_ln) + ' bp'
#print type(os.path.basename(__file__))
#file_name='input_DNA.txt'
try:
hand=open(file_name)
except:
print "Error! The specified file could not be opened. Using the defile input file option: "+default_file_name
hand=open(default_file_name)
dataset=hand.read()
hand.close()
#Cleaning the data
dataset_cln=dataset
dataset_cln=dataset_cln.strip().upper()
dataset_lst=dataset_cln.split('\n')
dataset_cln=''.join(dataset_lst)
#print len(dataset)
print 'We are working with the dataset of '+ str(len(dataset_cln))+' characters....'
#print k_mer_ln
if len(dataset_cln) > k_mer_ln:
results=frequent_patterns(dataset_cln,k_mer_ln)
else:
print "\nError! k-mer length should be less than number of characters in the DNA dataset"
print "Please try changing the input parameters"
return
# print results
if max(results.values())==1:
print "No motif occurs more than once. Please try changing the input parameters"
elif len(results)==1:
print '\n'+'Single most frequent pattern found'+'\n'
print str(k_mer_ln)+" bp motif "+results.keys()[0]+" occurs "+str(results.values()[0])+" times in the input DNA sequence"
elif len(results)>1:
print '\n'+'No single most frequent pattern found'+'\n'
for item in results:
print str(k_mer_ln)+" bp motif "+item+" occurs "+str(results[item])+" times in the input DNA sequence"
else:
print "No results found. Please try changing the input parameters"
def main(argv):
inputfile = ''
file_name = ''
k_mer_arg=''
default_file_name='input_DNA.txt'
k_mer_ln=10 #default value for the length of the pattern
try:
opts, args = getopt.getopt(argv,"hi:k:")
except getopt.GetoptError:
print 'test.py -i <inputfile> -k <k-mer length>'
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print 'Usage: test.py -i <inputfile> -k <k-mer length>'
sys.exit()
elif opt in ("-i"):
inputfile = arg
elif opt in ("-k"):
k_mer_arg = arg
if int(k_mer_arg)>0:
k_mer_ln=int(k_mer_arg)
print 'Length of k-mer is '+ str(k_mer_ln)+' bp'
else:
print 'Using default k-mer length of '+str(k_mer_ln) + ' bp'
if (len(inputfile))>0:
file_name=inputfile
print 'Using DNA inputfile: '+inputfile
else:
file_name=default_file_name
print 'Using default inputfile: '+file_name
# print 'hehe'
#file_name='input_DNA.txt'
hand=open(file_name)
dataset=hand.read()
hand.close()
#Cleaning the data
dataset_cln=dataset
dataset_cln=dataset_cln.strip().upper()
dataset_lst=dataset_cln.split('\n')
dataset_cln=''.join(dataset_lst)
#print len(dataset)
print 'We are working with the dataset of '+ str(len(dataset_cln))+' characters....'
#print k_mer_ln
results=frequent_patterns(dataset_cln,k_mer_ln)
if len(results)==1:
print '\n'+'Single most frequent pattern found'+'\n'
print str(k_mer_ln)+" bp motif "+results.keys()[0]+" occurs "+str(results.values()[0])+" times in the input DNA sequence"
elif len(results)>1:
print '\n'+'No single most frequent pattern found'+'\n'
for item in results:
print str(k_mer_ln)+" bp motif "+item+" occurs "+str(results[item])+" times in the input DNA sequence"