# Path: alfpy/graphdna.py
# def _2DSGraphVector(seq):
# def _2DMGraphVector(seq, n):
# def _2DNGraphVector(genomeseq):
# def create_2DSGraphVectors(seq_records):
# def create_2DMGraphVectors(seq_records, n):
# def create_2DNGraphVectors(seq_records):
#     def __init__(self, vector, disttype='euclid_norm'):
# def main():
# class Distance(distance.Distance):
# 
# Path: alfpy/utils/distmatrix.py
# def create(id_list, distance):
# def read_highcharts_matrix(id_list, data):
#     def __init__(self, id_list, data):
#     def normalize(self):
#     def __iter__(self):
#     def writer(self, handle, f, decimal_places):
#     def display(self, f="phylip", decimal_places=7):
#     def write_to_file(self, handle, f="phylip", decimal_places=7):
#     def highcharts(self):
#     def format(self, decimal_places=7):
#     def min(self):
#     def max(self):
#     def is_zero(self):
#     def __repr__(self):
# class Matrix():


import numpy as np
import unittest
from alfpy import graphdna
from alfpy.utils import distmatrix
from . import utils
        vec = graphdna._2DMGraphVector(seq, 5)
        exp = [15, 12.14790682, 13.5804606, 15.88980624, 19.16010756]
        self.assertEqual(vec.shape, (5,))
        self.assertTrue(np.allclose(vec, np.array(exp)))

    def test_2DNGraphVector(self):
        seq = 'CTAGGGAACATACCA'
        vec = graphdna._2DNGraphVector(seq)
        md5 = utils.calc_md5(vec)
        self.assertEqual(len(vec), 48)
        self.assertEqual(md5, '44829cc0277531646d656cdaacd3ae94')

    def test_2DNGraphVector_ambiguousDNA(self):
        seq = 'CTAGGGAACATACCA'
        vec = graphdna._2DNGraphVector(seq)
        md5 = utils.calc_md5(vec)
        self.assertEqual(len(vec), 48)
        self.assertEqual(md5, '44829cc0277531646d656cdaacd3ae94')

    def test_create_2DSGraphVectors(self):
        data = graphdna.create_2DSGraphVectors(self.dna_records)
        md5 = utils.calc_md5(data)
        self.assertEqual(md5, 'e2399897bb7eaa5ca3a81c84e2eeac84')

    def test_create_2DMGraphVectors(self):
        data = graphdna.create_2DMGraphVectors(self.dna_records, 10)
        md5 = utils.calc_md5(data)
        self.assertEqual(md5, '8c7d4dca912aeaf7c88d325799dadf00')

    def test_create_2DNGraphVectors(self):

# Path: alfpy/graphdna.py
# def _2DSGraphVector(seq):
# def _2DMGraphVector(seq, n):
# def _2DNGraphVector(genomeseq):
# def create_2DSGraphVectors(seq_records):
# def create_2DMGraphVectors(seq_records, n):
# def create_2DNGraphVectors(seq_records):
#     def __init__(self, vector, disttype='euclid_norm'):
# def main():
# class Distance(distance.Distance):
# 
# Path: alfpy/utils/distmatrix.py
# def create(id_list, distance):
# def read_highcharts_matrix(id_list, data):
#     def __init__(self, id_list, data):
#     def normalize(self):
#     def __iter__(self):
#     def writer(self, handle, f, decimal_places):
#     def display(self, f="phylip", decimal_places=7):
#     def write_to_file(self, handle, f="phylip", decimal_places=7):
#     def highcharts(self):
#     def format(self, decimal_places=7):
#     def min(self):
#     def max(self):
#     def is_zero(self):
#     def __repr__(self):
# class Matrix():


# Path: tests/test_graphdna.py
import numpy as np
import unittest
from alfpy import graphdna
from alfpy.utils import distmatrix
from . import utils

        vec = graphdna._2DMGraphVector(seq, 5)
        exp = [15, 12.14790682, 13.5804606, 15.88980624, 19.16010756]
        self.assertEqual(vec.shape, (5,))
        self.assertTrue(np.allclose(vec, np.array(exp)))

    def test_2DNGraphVector(self):
        seq = 'CTAGGGAACATACCA'
        vec = graphdna._2DNGraphVector(seq)
        md5 = utils.calc_md5(vec)
        self.assertEqual(len(vec), 48)
        self.assertEqual(md5, '44829cc0277531646d656cdaacd3ae94')

    def test_2DNGraphVector_ambiguousDNA(self):
        seq = 'CTAGGGAACATACCA'
        vec = graphdna._2DNGraphVector(seq)
        md5 = utils.calc_md5(vec)
        self.assertEqual(len(vec), 48)
        self.assertEqual(md5, '44829cc0277531646d656cdaacd3ae94')

    def test_create_2DSGraphVectors(self):
        data = graphdna.create_2DSGraphVectors(self.dna_records)
        md5 = utils.calc_md5(data)
        self.assertEqual(md5, 'e2399897bb7eaa5ca3a81c84e2eeac84')

    def test_create_2DMGraphVectors(self):
        data = graphdna.create_2DMGraphVectors(self.dna_records, 10)
        md5 = utils.calc_md5(data)
        self.assertEqual(md5, '8c7d4dca912aeaf7c88d325799dadf00')

    def test_create_2DNGraphVectors(self):

        data = graphdna.create_2DNGraphVectors(self.dna_records)