def create_gst_on_file(filename, gprint=False, strip=False):
"""
Opens a file and create a suffix tree on every string
"""
st = SuffixTree()
print "Opening file \"{0}\".".format(filename)
time_start = default_timer()
with open(filename) as text_file:
i = -1
for line in text_file:
st.add_string(line.strip() if strip else line)#.strip())#.strip())
i += 1
if i % 100000 == 0:
print "\tProcessed {0} elements".format(i)
if gprint:
g = Grapher(st)
g.createGraphviz()
print "Suffix tree for \"{0}\" complete in {1} seconds".format(filename, default_timer() - time_start)
return st
def length_distribution_on_suffix(filename, adaptersequence):
st = SuffixTree()
number_of_matches = 0
length_distribution = {}
#Reverse adaptersequence to create prefixtree
reversed_adaptersequence = adaptersequence[::-1]
st.add_string(reversed_adaptersequence)
#Loop through the sequences in the file
for line in generate_strings(filename):
reversed_line = line[::-1]
#Get longest suffix-prefix match for given string
longest_match = st.find_prefixmatch_nr(reversed_line, st.root, 0.0)
#Check number of matches
length_match = len(longest_match)
if length_match > 0:
number_of_matches += 1
length_rest = len(line) - length_match
if length_rest in length_distribution:
length_distribution[length_rest] += 1
else:
length_distribution[length_rest] = 1
return number_of_matches, length_distribution
