# #Get Features of the Fragments count = 0 for j in fragmentedSeqs[i]: temp = [] something = [] # j is the fragment count +=1 # print j #Bases Frequencies #findBasesFrequency(j) = Afrequency, Tfrequency, Gfrequency, Cfrequency temp = findBasesFrequency(j) #line = np.hstack((line, temp)) # print "temp", temp # print "temp size", len(temp) # print "" dimers,trimers,dimercounts,trimercounts = find_kmers(j) # print "dimers",dimers # print "j",j # print "dimercounts",dimercounts # exit() maxNoDimers = float(windowSize-1) # The length of each window is 10 maxNoTrimers = float(windowSize-2)
from myfunctions import findBasesFrequency
a = 'CCTTCTTCTTTCTTAAAAAGTCTTAGTACGATTGACCAAGTCAGAAAAAAAAAAAAAAAGGAACTAAAAAAAGTTTTAATTAATTATGAGAGCTTTGGCATATTTCAAGAAGGGTGATATTCACTT'
Afrequency, Tfrequency, Gfrequency, Cfrequency = findBasesFrequency(a)
print Afrequency, Tfrequency, Gfrequency, Cfrequency
exit()
# print range(5)
# print ""
# for i in range(10):
# print "i", i
# if i in range(5):
# print "yes"
# print ""
# exit()
import numpy as np
sortedArray = np.load('Gritsenko/sortedArray.npy')
print "sortedArray loaded, is the actualArrayWithNames Array (without the names) sorted by Init Rates: ", sortedArray.shape
temp = sortedArray[:,2].astype(int) # LEnGTH
maxLength=temp.max(axis=0)
print "maxLength", maxLength # Find max length
minLength=temp.min(axis=0)
print "minLength", minLength
print ""
arrayEsetA = []
arrayEsetT = []
arrayEsetG = []
arrayEsetC = []
#Pass from every position
