Пример #1
0
def test_query():
    """
	Function to test that a query returns the correct result. Inserts
	a known value then queries for that value, assert that the returned value is the
	same as the inserted value.
	"""
    stub = dgraph.create_client_stub()
    client = dgraph.create_client(stub)
    dgraph.drop_all(client)
    dgraph.add_schema(client)
    dgraph.add_genome_to_schema(client, "test_genome")

    kmers = {"genome": ["AAAA", "TTTT", "CCCC", "GGGG"]}
    dgraph.add_kmers_dgraph(client, kmers, "test_genome")

    sg1 = dgraph.example_query(client, "test_genome")

    kmer_list = []
    for x in sg1:
        if x == sg1[-1]:
            dict = sg1[-1]
            value = list(dict.values())
            kmer = value[0]
            last_kmer = kmer[0]
            kmer_list.append(last_kmer["kmer"])
        else:
            kmer = x["kmer"]
            kmer_list.append(kmer)
    print(kmer_list)
    for i, x in enumerate(kmer_list):
        assert x == kmers["genome"][i]
Пример #2
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def main():
    """
    The program - The work horse
    :return: success
    """
    path = os.path.abspath("data/genomes/test/")
    output_directory = os.path.abspath("data/logger")
    print(path)
    # setup the application logging
    LOG = logging_functions.create_logger()

    fh = logging.FileHandler(
        os.path.join(output_directory, 'pans_labyrinth.log'), 'w', 'utf-8')
    LOG.addHandler(fh)

    #options = commandline.arg_parser(client)
    #dgraph.execute_args(client, options)

    #LOG.debug(options)
    LOG.info("Starting pans_labyrinth")
    stub = dgraph.create_client_stub()
    client = dgraph.create_client(stub)
    dgraph.drop_all(client)
    dgraph.add_schema(client)

    LOG.info("Starting to create graph")
    for filepath in files.walkdir(path):
        with open(filepath, 'rb') as file:
            dgraph.create_graph(client, file, filepath)

    stub.close()
    LOG.info("ALL DONE")
Пример #3
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def test_non_fasta():
    """
	Function to test that the program only accepts .fasta files. Could
	create issues if the program was reading non-fasta files and inserting the
	values into the graph.
	"""
    path = os.path.abspath("pans_labyrinth/tests/data/bad_fasta")
    with pytest.raises(SystemExit) as se:
        stub = dgraph.create_client_stub()
        client = dgraph.create_client(stub)
        dgraph.drop_all(client)
        dgraph.add_schema(client)
        for filepath in files.walkdir(path):
            with open(filepath, 'rb') as file:
                dgraph.create_graph(client, file, filepath)
    assert se.type == SystemExit
Пример #4
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def test_no_file():
    """
	Function to ensure that if no file is present in the given directory then
	The program fails.
	"""
    path = os.path.abspath("pans_labyrinth/tests/data/empty_test")
    with pytest.raises(SystemExit) as se:
        stub = dgraph.create_client_stub()
        client = dgraph.create_client(stub)
        dgraph.drop_all(client)
        dgraph.add_schema(client)
        dgraph.add_genome_to_schema(client, "test_genome")
        for filepath in files.walkdir(path):
            with open(filepath, 'rb') as file:
                dgraph.create_graph(client, file, filepath)
    assert se.type == SystemExit
Пример #5
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def test_hash_verification():
    path = os.path.abspath("pans_labyrinth/tests/data/contig_test")
    stub = dgraph.create_client_stub()
    client = dgraph.create_client(stub)
    dgraph.drop_all(client)
    dgraph.add_schema(client)
    for filepath in files.walkdir(path):
        with open(filepath, 'rb') as file:
            x = 0
            filename = file.name
            genome = "genome_" + commandline.compute_hash(filepath)
            dgraph.add_genome_to_schema(client, genome)
            all_kmers = dgraph.get_kmers_files(filename, 11)
            dgraph.add_kmers_dgraph(client, all_kmers, genome)

    assert genome == "genome_" + commandline.compute_hash(filepath)
Пример #6
0
def test_verify_contig():
    """
	A test to verify that the kmers returned from the graph are the same as the
	kmers in the original contig
	"""

    #Create graph and fill it with kmers from a fasta file
    path = os.path.abspath("pans_labyrinth/tests/data/contig_test")
    stub = dgraph.create_client_stub()
    client = dgraph.create_client(stub)
    dgraph.drop_all(client)
    dgraph.add_schema(client)
    for filepath in files.walkdir(path):
        with open(filepath, 'rb') as file:
            x = 0
            filename = file.name
            genome = "genome_" + commandline.compute_hash(filepath)
            dgraph.add_genome_to_schema(client, genome)
            all_kmers = dgraph.get_kmers_files(filename, 11)
            dgraph.add_kmers_dgraph(client, all_kmers, genome)

    #Query graph and put all kmers into a list
    sg1 = dgraph.path_query(client, genome)

    kmer_list = []
    for i, x in enumerate(sg1["path"]):
        kmer = sg1["path"][i]["kmer"]
        kmer_list.append(kmer)
    print(kmer_list)

    #Gets the whole first kmer in the list and then the last character of the rest of the kmers in the list
    #Creates a string representing the contig
    first, *rest = kmer_list
    ends = [kmer[-1] for kmer in rest]
    contig = ''.join([first] + ends)

    #Gets the actual contig from the fasta file and turns it into  string
    with open(path + "/test.fasta", "r") as f:
        for record in SeqIO.parse(f, "fasta"):
            sequence = record.seq
    sequence_string = str(sequence)

    assert contig == sequence_string[:-1]