test_functions.py

# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2010-2015, Michigan State University.
# Copyright (C) 2015-2016, The Regents of the University of California.
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# Contact: khmer-project@idyll.org
# pylint: disable=missing-docstring,invalid-name,no-member

import screed
import khmer
import os
import sys
import pytest
from . import khmer_tst_utils as utils

from khmer.kfile import check_input_files, get_file_writer
try:
    from StringIO import StringIO
except ImportError:
    from io import StringIO


def test_forward_hash():
    assert khmer.forward_hash('AAAA', 4) == 0
    assert khmer.forward_hash('TTTT', 4) == 0
    assert khmer.forward_hash('CCCC', 4) == 170
    assert khmer.forward_hash('GGGG', 4) == 170

    h = 13607885392109549066
    assert khmer.forward_hash('GGTTGACGGGGCTCAGGGGGCGGCTGACTCCG', 32) == h


def test_get_file_writer_fail():
    somefile = utils.get_temp_filename("potato")
    somefile = open(somefile, "w")
    stopped = True
    try:
        get_file_writer(somefile, True, True)
        stopped = False
    except ValueError as err:
        assert "Cannot specify both bzip and gzip" in str(err), str(err)

    assert stopped, "Expected exception"


def test_forward_hash_no_rc():
    h = khmer.forward_hash_no_rc('AAAA', 4)
    assert h == 0, h

    h = khmer.forward_hash_no_rc('TTTT', 4)
    assert h == 85, h

    h = khmer.forward_hash_no_rc('CCCC', 4)
    assert h == 170, h

    h = khmer.forward_hash_no_rc('GGGG', 4)
    assert h == 255, h


def test_reverse_hash():
    s = khmer.reverse_hash(0, 4)
    assert s == "AAAA"

    s = khmer.reverse_hash(85, 4)
    assert s == "TTTT"

    s = khmer.reverse_hash(170, 4)
    assert s == "CCCC"

    s = khmer.reverse_hash(255, 4)
    assert s == "GGGG"


def test_reverse_complement():
    s = 'AATTCCGG'
    assert khmer.reverse_complement(s) == 'CCGGAATT'

    s = 'A'
    assert khmer.reverse_complement(s) == 'T'
    s = 'T'
    assert khmer.reverse_complement(s) == 'A'
    s = 'C'
    assert khmer.reverse_complement(s) == 'G'
    s = 'G'
    assert khmer.reverse_complement(s) == 'C'


def test_reverse_complement_exception():
    # deal with DNA, ignore rest
    assert khmer.reverse_complement('FGF') == 'FCF'


def test_reverse_hash_longs():
    # test explicitly with long integers, only needed for python2
    # the builtin `long` exists in the global scope only
    global long  # pylint: disable=global-variable-undefined
    if sys.version_info > (3,):
        long = int

    s = khmer.reverse_hash(long(0), 4)
    assert s == "AAAA"

    s = khmer.reverse_hash(long(85), 4)
    assert s == "TTTT"

    s = khmer.reverse_hash(long(170), 4)
    assert s == "CCCC"

    s = khmer.reverse_hash(long(255), 4)
    assert s == "GGGG"


def test_reverse_hash_raises():
    with pytest.raises(TypeError) as excinfo:
        khmer.reverse_hash('2345', 4)

    assert 'int' in str(excinfo.value)


def test_hash_murmur3():
    assert khmer.hash_murmur3('AAAA') == 526240128537019279
    assert khmer.hash_murmur3('TTTT') == 526240128537019279
    assert khmer.hash_murmur3('CCCC') == 14391997331386449225
    assert khmer.hash_murmur3('GGGG') == 14391997331386449225
    assert khmer.hash_murmur3('TATATATATATATATATATA') != 0
    assert khmer.hash_murmur3('TTTTGCAAAA') != 0
    assert khmer.hash_murmur3('GAAAATTTTC') != 0


def test_hash_no_rc_murmur3():
    h = khmer.hash_no_rc_murmur3('AAAA')
    assert h == 5231866503566620412, h

    h = khmer.hash_no_rc_murmur3('TTTT')
    assert h == 5753003579327329651, h

    h = khmer.hash_no_rc_murmur3('CCCC')
    assert h == 3789793362494378039, h

    h = khmer.hash_no_rc_murmur3('GGGG')
    assert h == 17519752047064575358, h


def test_get_primes():
    primes = khmer.get_n_primes_near_x(7, 20)

    assert primes == [19, 17, 13, 11, 7, 5, 3]

    primes_not_float = khmer.get_n_primes_near_x(7, 20.)

    assert primes_not_float == [19, 17, 13, 11, 7, 5, 3]
    assert all(isinstance(p, int) for p in primes_not_float)


def test_get_primes_fal():
    try:
        khmer.get_n_primes_near_x(5, 5)
        assert 0, "previous statement should fail"
    except RuntimeError as err:
        assert "unable to find 5 prime numbers < 5" in str(err)


def test_extract_countgraph_info_badfile():
    try:
        khmer.extract_countgraph_info(
            utils.get_test_data('test-abund-read-2.fa'))
        assert 0, 'this should fail'
    except ValueError:
        pass


def test_extract_countgraph_info():
    fn = utils.get_temp_filename('test_extract_counting.ct')
    for size in [1e6, 2e6, 5e6, 1e7]:
        ht = khmer.Countgraph(25, size, 4)
        ht.save(fn)

        try:
            info = khmer.extract_countgraph_info(fn)
        except ValueError as err:
            assert 0, 'Should not throw a ValueErorr: ' + str(err)
        ksize, n_tables, table_size, _, _, _, _ = info
        print(ksize, table_size, n_tables)

        assert(ksize) == 25
        assert table_size == size
        assert n_tables == 4

        try:
            os.remove(fn)
        except OSError as err:
            assert 0, '...failed to remove ' + fn + str(err)


def test_extract_nodegraph_info_badfile():
    try:
        khmer.extract_nodegraph_info(
            utils.get_test_data('test-abund-read-2.fa'))
        assert 0, 'this should fail'
    except ValueError:
        pass


def test_extract_nodegraph_info():
    fn = utils.get_temp_filename('test_extract_nodegraph.pt')
    for size in [1e6, 2e6, 5e6, 1e7]:
        ht = khmer.Nodegraph(25, size, 4)
        ht.save(fn)

        info = khmer.extract_nodegraph_info(fn)
        ksize, table_size, n_tables, _, _, _ = info
        print(ksize, table_size, n_tables)

        assert(ksize) == 25
        assert table_size == size, table_size
        assert n_tables == 4

        try:
            os.remove(fn)
        except OSError as err:
            print('...failed to remove {fn}'.format(fn) + str(err),
                  file=sys.stderr)


def test_check_file_status_kfile():
    fn = utils.get_temp_filename('thisfiledoesnotexist')

    old_stderr = sys.stderr
    sys.stderr = capture = StringIO()

    try:
        check_input_files(fn, False)
    except SystemExit:
        assert "does not exist" in capture.getvalue(), capture.getvalue()
    finally:
        sys.stderr = old_stderr


def test_check_file_status_kfile_force():
    fn = utils.get_temp_filename('thisfiledoesnotexist')

    old_stderr = sys.stderr
    sys.stderr = capture = StringIO()

    try:
        check_input_files(fn, True)
    except OSError:
        assert False
    finally:
        sys.stderr = old_stderr

    assert "does not exist" in capture.getvalue(), capture.getvalue()