def test_stats_dict():
#Stats = collections.namedtuple('FastaStats', ['nreads', 'total', 'n50', 'p95'])
stats_raw_reads = M.Stats(100, 1000, 50, 95)
stats_seed_reads = M.Stats(50, 500, 25, 40)
stats_corrected_reads = M.Stats(10, 100, 5, 9)
genome_length = 19
length_cutoff = 10
result = M.stats_dict(stats_raw_reads, stats_seed_reads, stats_corrected_reads, genome_length, length_cutoff)
expected = {
'genome_length': 19,
'length_cutoff': 10,
'preassembled_bases': 100,
'preassembled_coverage': 5.263,
'preassembled_mean': 10.0,
'preassembled_n50': 5,
'preassembled_p95': 9,
'preassembled_reads': 10,
'preassembled_yield': 0.2,
'raw_bases': 1000,
'raw_coverage': 52.632,
'raw_mean': 10.0,
'raw_n50': 50,
'raw_p95': 95,
'raw_reads': 100,
'seed_bases': 500,
'seed_coverage': 26.316,
'seed_mean': 10.0,
'seed_n50': 25,
'seed_p95': 40,
'seed_reads': 50}
helpers.equal_dict(result, expected)
def test_stats_dict():
#Stats = collections.namedtuple('FastaStats', ['nreads', 'total', 'n50', 'p95'])
stats_raw_reads = M.Stats(100, 1000, 50, 95, 0.0)
stats_seed_reads = M.Stats(50, 500, 25, 40, 0.0)
stats_corrected_reads = M.Stats(10, 100, 5, 9, 0.0)
genome_length = 19
length_cutoff = 10
frag = 1.0
trunc = 2.5
result = M.stats_dict(stats_raw_reads, stats_seed_reads,
stats_corrected_reads, genome_length, length_cutoff,
frag, trunc)
expected = {
'genome_length': 19,
'length_cutoff': 10,
'preassembled_bases': 100,
'preassembled_coverage': 5.263,
'preassembled_mean': 10.0,
'preassembled_n50': 5,
'preassembled_p95': 9,
'preassembled_reads': 10,
'preassembled_seed_fragmentation': 1.0,
'preassembled_seed_truncation': 2.5,
'preassembled_yield': 0.2,
'preassembled_esize': 0.0,
'raw_bases': 1000,
'raw_coverage': 52.632,
'raw_mean': 10.0,
'raw_n50': 50,
'raw_p95': 95,
'raw_reads': 100,
'raw_esize': 0.0,
'seed_bases': 500,
'seed_coverage': 26.316,
'seed_mean': 10.0,
'seed_n50': 25,
'seed_p95': 40,
'seed_reads': 50,
'seed_esize': 0.0,
}
helpers.equal_dict(result, expected)
def test_mapped_readlengths_from_dbdump_output():
mapped = f.mapped_readlengths_from_dbdump_output(sample_DBdump_output)
helpers.equal_dict(mapped, {0: 2000, 1: 2000, 2: 2500})
def test_mapped_readlengths_from_dbdump_output():
mapped = f.mapped_readlengths_from_dbdump_output(sample_DBdump_output)
helpers.equal_dict(mapped, {0: 2000, 1: 2000, 2: 2500})
