Winterflower

"""
Simple RxPy example
"""

from rx import Observer, Observable
from numpy import random

class DataAnalyser(Observer):
    #a class for analyzing data
    def on_next(self, value):

Winterflower

"""Demonstrates how to construct and send raw Ethernet packets on the
network.

You probably need root privs to be able to bind to the network interface,
e.g.:

    $ sudo python sendeth.py
"""

from socket import *

Winterflower

try:
        from shogun.PreProc import SortWordString, SortUlongString
except ImportError:
        from shogun.Preprocessor import SortWordString, SortUlongString
from shogun.Kernel import CommWordStringKernel, CommUlongStringKernel, \
                CombinedKernel

from shogun.Features import StringWordFeatures, StringUlongFeatures, \
                StringCharFeatures, CombinedFeatures, DNA, Labels
from shogun.Classifier import MSG_INFO, MSG_ERROR

Winterflower

from modshogun import StringCharFeatures,DNA
from modshogun import StringWordFeatures

#training set
train_dna=['ACGTGT',
            'ACGGTT',
            'AGTGTT',
        'ACCGGT',
        'TGTGTA',
        'TTGGGT']

Winterflower

from itertools import product
for roll in product(['A','C','T','G'], repeat = 6):
    print(roll)

allkmers=[]

kmers=product(['A','C','T','G'],repeat=6)

Winterflower

# -*- coding: utf-8 -*-
#make a tree of all the possible kmers in a given alphabet 

#this method creates a subtree given an alphabet and a parentnode 
def maketree(alphabet,parentnode):
  for letter in alphabet:
    parentnode.append([letter])
  return parentnode

print "======================TESTING METHOD: MAKETREE==================="

Winterflower

# -*- coding: utf-8 -*-
def kmer(sequence,k):
  length=len(sequence)
 #if the kmer size if greater than the lenght of the sequene
  if k>=length:
    print "You specified a kmer size, which if greater or equal to the length of the sequence"
    return 
  stepsize=k-1
  i=0
  kmers=[]

Winterflower

# -*- coding: utf-8 -*-
def kmer(sequence,k):
  length=len(sequence)
 #if the kmer size if greater than the lenght of the sequene
  if k>=length:
    print "You specified a kmer size, which if greater or equal to the length of the sequence"
    return 
  stepsize=k-1
  i=0
  kmers=[]