Python get_stats_from_contigs Examples

Example #1

def test_get_column_stats():
    stats = assembly.get_stats_from_contigs(fasta_file)
    data = stats['GC']
    stats = assembly.get_column_stats(data)

    assert floor(stats['mean']) == 39
    assert floor(stats['median']) == 37

Example #2

File: test_30_assembly.py Project: jmeppley/py-metagenomics

def test_get_column_stats():
    stats = assembly.get_stats_from_contigs(fasta_file)
    data = stats['GC']
    stats = assembly.get_column_stats(data)

    assert floor(stats['mean'])==39
    assert floor(stats['median'])==37

Example #3

def test_get_stats_from_contigs():
    stats = assembly.get_stats_from_contigs(fasta_file)

    # its a data frame
    assert isinstance(stats, pandas.core.frame.DataFrame)

    # 100 x 2
    assert stats.shape == (100, 2)

    # test a couple arbitrary values
    assert stats.loc['000005_1741_3371', 'GC'] == 32.8125
    assert stats.loc['000483_1123_3166', 'length'] == 269

Example #4

File: test_30_assembly.py Project: jmeppley/py-metagenomics

def test_get_stats_from_contigs():
    stats = assembly.get_stats_from_contigs(fasta_file)

    # its a data frame
    assert isinstance(stats, pandas.core.frame.DataFrame)

    # 100 x 2
    assert stats.shape == (100,2)

    # test a couple arbitrary values
    assert stats.loc['000005_1741_3371','GC'] == 32.8125
    assert stats.loc['000483_1123_3166','length'] == 269