debruijn-tp/tests/test_construction_debruijn.py

"""Tests for graph build"""
import pytest
import os
import networkx as nx
import pickle
from .context import debruijn
#from .context import debruijn_comp
from debruijn import read_fastq
from debruijn import cut_kmer
from debruijn import build_kmer_dict
from debruijn import build_graph


def test_read_fastq():
    """Test fastq reading"""
    fastq_reader = read_fastq(os.path.abspath(os.path.join(os.path.dirname(__file__), "test_two_reads.fq")))
    assert next(fastq_reader) == "TCAGAGCTCTAGAGTTGGTTCTGAGAGAGATCGGTTACTCGGAGGAGGCTGTGTCACTCATAGAAGGGATCAATCACACCCACCACGTGTACCGAAACAA"
    assert next(fastq_reader) == "TTTGAATTACAACATCCATATGTTCTTGATGCTGGAATTCCAATATCTCAGTTGACAGTGTGCCCTCACCAGTGGATCAATTTACGAACCAACAATTGTG"


def test_cut_kmer():
    """test Kmer cut"""
    kmer_reader = cut_kmer("TCAGA", 3)
    assert next(kmer_reader) == "TCA"
    assert next(kmer_reader) == "CAG"
    assert next(kmer_reader) == "AGA"


def test_build_kmer_dict():
    kmer_dict = build_kmer_dict(os.path.abspath(os.path.join(os.path.dirname(__file__), "test_build.fq")), 3)
    assert(len(kmer_dict.keys()) == 4)
    assert "TCA" in kmer_dict
    assert "CAG" in kmer_dict
    assert "AGA" in kmer_dict
    assert "GAG" in kmer_dict
    assert kmer_dict["AGA"] == 2

def test_build_graph():
    file = open(os.path.abspath(os.path.join(os.path.dirname(__file__), "kmer.pck")),'rb')
    kmer_dict = pickle.load(file)
    graph = build_graph(kmer_dict)
    #TCAGAGA
    #TCA  TC CA
    #CAG CA AG
    #AGA AG GA
    #GAG GA AG
    #AGA AG GA
    assert graph.number_of_nodes() == 4
    assert graph.number_of_edges() == 4
    assert "AG" in graph
    assert "GA" in graph
    assert graph.edges["AG", "GA"]['weight'] == 2

# def test_build_graph_comp():
#     file = open(os.path.abspath(os.path.join(os.path.dirname(__file__), "kmer_comp.pck")),'rb')
#     kmer_dict = pickle.load(file)
#     graph = build_graph(kmer_dict)
#     #TCAGAGA
#     #TCA  TC CA
#     #CAG CA AG
#     #AGA AG GA
#     #GAG GA AG
#     #AGA AG GA
#     # ((TC, AG), (CA, GT)), (CA, AG), (AG
#     assert graph.number_of_nodes() == 4
#     assert graph.number_of_edges() == 3
#     assert "AG" in graph
#     assert "GA" in graph
#     assert graph.edges["AG", "GA"]['weight'] == 2