def test_get_min_coverage_spades_1(self, mock_contigs_spades_1):
# Should return 24.26 for `mock_contigs_spades_1`
contig_collection, overlap_collection = mock_contigs_spades_1
cov_calc: CovCalc = sts.CoverageCalculator(contig_collection)
expected_min_cov: float = 24.26
assert abs(cov_calc.get_min_coverage() - expected_min_cov) < 1e-2
def test_get_min_coverage_a5_0(self, mock_contigs_a5_0):
# Should return None for `mock_contigs_a5_0`
contig_collection, overlap_collection = mock_contigs_a5_0
cov_calc: CovCalc = sts.CoverageCalculator(contig_collection)
expected_min_cov: float = None
assert cov_calc.get_min_coverage() is expected_min_cov
def test_get_min_coverage_spades_0(self, mock_contigs_spades_0):
# Should return 18.28 for `mock_contigs_spades_0`
contig_collection, overlap_collection = mock_contigs_spades_0
cov_calc: CovCalc = sts.CoverageCalculator(contig_collection)
expected_min_cov: float = 18.28
assert abs(cov_calc.get_min_coverage() - expected_min_cov) < 1e-2
def test_get_median_coverage_spades_no_multplty_0_0(self, mock_contigs_spades_no_multplty_0):
# Should return 23.48 for `mock_contigs_spades_no_multplty_0`
contig_collection, overlap_collection = mock_contigs_spades_no_multplty_0
cov_calc: CovCalc = sts.CoverageCalculator(contig_collection)
expected_median_cov: float = 23.48
assert abs(cov_calc.calc_median_coverage() - expected_median_cov) < 1e-2
def test_get_max_coverage_mix_0(self, mock_contigs_mix_0):
# Should return 28.68 for `mock_contigs_mix_0`
contig_collection, overlap_collection = mock_contigs_mix_0
cov_calc: CovCalc = sts.CoverageCalculator(contig_collection)
expected_max_cov: float = 28.68
assert abs(cov_calc.get_max_coverage() - expected_max_cov) < 1e-2
def test_filter_non_none_covs_spades_no_multiplty_0(self, mock_contigs_spades_no_multplty_0):
# Should find 4 "coverage-containing" contigs in `mock_contigs_spades_no_multplty_0`
contig_collection, overlap_collection = mock_contigs_spades_no_multplty_0
cov_calc: CovCalc = sts.CoverageCalculator(contig_collection)
expected_len: int = 4
assert len(cov_calc._coverages) == expected_len
def test_filter_non_none_covs_spades_1(self, mock_contigs_spades_1):
# Should find 7 "coverage-containing" contigs in `mock_contigs_spades_1`
contig_collection, overlap_collection = mock_contigs_spades_1
cov_calc: CovCalc = sts.CoverageCalculator(contig_collection)
expected_len: int = 7
assert len(cov_calc._coverages) == expected_len
def write_summary(contig_collection: ContigCollection,
overlap_collection: OverlapCollection, infpath: str,
outdpath: str, out_prefix: str) -> None:
# Function writes summary to summary file.
#
# :param contig_collection: instance of ContigCollection returned by
# `src.contigs.get_contig_collection` function;
# :param overlap_collection: instance of OverlapCollection returned by
# `src.overlaps.detect_adjacent_contigs` function;
# :param infpath: path to input file (it will be mentioned in summary);
# :param outdpath: path to output directory;
# :param out_prefix: prefix for current output files;
# Make path to summary file
summary_fpath: str = os.path.join(
outdpath,
'{}_combinator_summary_FQ.txt'\
.format(out_prefix)
)
print('Writing summary to `{}`'.format(summary_fpath))
# Proceed
wrk_str: str
outfile: TextIO
with open(summary_fpath, 'w') as outfile:
# Path to input file
outfile.write('Input file: `{}`\n\n'.format(infpath))
# Summary with some statistics:
_double_write(' === Summary ===', outfile)
# Number of contigs processed:
wrk_str = '{} contigs were processed.'.format(len(contig_collection))
_double_write(wrk_str, outfile)
# Sum of contigs' lengths
wrk_str = 'Sum of contig lengths: {} bp'\
.format(sts.calc_sum_contig_lengths(contig_collection))
_double_write(wrk_str, outfile)
# Expected length of the genome
wrk_str = 'Expected length of the genome: {} bp'\
.format(sts.calc_exp_genome_size(contig_collection, overlap_collection))
_double_write(wrk_str, outfile)
# Calculate coverage statistics
cov_calc = sts.CoverageCalculator(contig_collection)
# Min coverage
min_coverage: float = cov_calc.get_min_coverage()
wrk_str = 'Min coverage: {}'\
.format(min_coverage if not min_coverage is None else 'NA')
_double_write(wrk_str, outfile)
# Max coverage
max_coverage: float = cov_calc.get_max_coverage()
wrk_str = 'Max coverage: {}'\
.format(max_coverage if not max_coverage is None else 'NA')
_double_write(wrk_str, outfile)
# Mean coverage
mean_coverage: float = cov_calc.calc_mean_coverage()
wrk_str = 'Mean coverage: {}'\
.format(mean_coverage if not mean_coverage is None else 'NA')
_double_write(wrk_str, outfile)
# Median coverage
median_coverage: float = cov_calc.calc_median_coverage()
wrk_str = 'Median coverage: {}'\
.format(median_coverage if not median_coverage is None else 'NA')
_double_write(wrk_str, outfile)
# LQ coefficient
wrk_str = 'LQ-coefficient: {}'\
.format(sts.calc_lq_coef(contig_collection, overlap_collection))
_double_write(wrk_str, outfile)
