def inputData():
    list = readFile.listFromInput()
    dnaName = list[0][1:]
    fastaDict, len = readFile.FASTAdictFromInput()
    dna = fastaDict[dnaName]
    del fastaDict[dnaName]
    return dna, fastaDict.values()

def run():
    listOfLines = readFile.listFromInput()
    print listOfLines
    text = listOfLines[0]
    k = int(listOfLines[1])
    result = frequentWords(text, k)
    print result
    readFile.lineToOutput(result)

def run():
    listOfLines = readFile.listFromInput()
    print listOfLines
    text = listOfLines[0]
    pattern = listOfLines[1]
    result = patternCount(text, pattern)
    print result
    readFile.lineToOutput(result)

def run():
    linesOfLines = readFile.listFromInput()
    print linesOfLines
    print "total " + str(len(linesOfLines[1]))
    output = occurrence(linesOfLines[0], linesOfLines[1])
    result = outputLine(output)
    print result
    readFile.lineToOutput(result)

def run():
    ids = readFile.listFromInput()
    result = ""
    for uniprot_id in ids:
        protein = Protein(uniprot_id)
        result += protein.fetch_motif(motifPattern())
    result = result.rstrip('\n')
    print result
    readFile.lineToOutput(result)

def run():
    listOfLines = readFile.listFromInput()
    mutations = 0
    strand1 = listOfLines[0]
    strand2 = listOfLines[1]
    for i in range(0, len(strand1)):
        if strand1[i] != strand2[i]:
            mutations += 1
    print mutations

def run():
    listOfLines = readFile.listFromInput()
    print listOfLines
    length = int(listOfLines[0])
    sequence = listOfLines[1].split(" ")
    search = sequenceSearch(sequence)
    print sequence
    #result = search.shortestSubsequence() + "\n"
    #result += search.longestSubsequence()
    #print result
    readFile.lineToOutput(result)

def run():
    listOfLines = readFile.listFromInput()
    alphabet = listOfLines[0].split(" ")
    print "Start"
    length = int(listOfLines[1])
    repeat_count = pow(len(alphabet), length)
    f = open('output.txt','w')
    is_new = True
    for result in alphabetGenerator(repeat_count, alphabet, length):
        if is_new:
            is_new = False
        else:
            f.write('\n')
        f.write(result)
    f.close()
    print "Done"

import sys, os
sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '../_common')))
sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '../bio_2')))

import readFile
import useful
import directedGraph as dG
import eulerianCycle as eC

lines = readFile.listFromInput()
Graph = dG.parseAsGraphSet(lines)
result = dG.nodesPathToLine(eC.findEulerianPath(Graph))
print result
readFile.lineToOutput(result)
    

import readFile
import parse
import useful
import deBruijnGraph

k, Text = readFile.listFromInput()
print k, Text
result = useful.lineFromObjectsCollection(deBruijnGraph.deBruijn(Text, int(k)))
print result
readFile.lineToOutput(result)
    

def run():
    listOfLines = readFile.listFromInput()
    prefixes, suffixes = prefixesAndSuffixes(listOfLines)
    result = zipPrefixesAndSuffixes(prefixes, suffixes)
    print result
    readFile.lineToOutput(result)

def run():
    listOfLines = readFile.listFromInput()
    maxRecord = recordsDictFromList(listOfLines)
    print "" + maxRecord.name + " \n" + str(maxRecord.data * 100)