def test_coverage_report_fixture_empty_coverage_file(self, tmpdir):
tmpdir = str(tmpdir)
coverage_file = write_empty_file(tmpdir + '/tmp.tab')
contig_file = write_empty_file(tmpdir + 'contigs.fasta')
output_file = write_empty_file(tmpdir + 'output.json')
with pytest.raises(ValueError) as exc:
args = gen_stats_report.parse_args(
['106000', contig_file, coverage_file, output_file, '500', 'metaspades'])
gen_stats_report.calc_coverage(args)
# Assert error comes from coverage file message, not fasta parsing error
assert 'Coverage file' in str(exc)
def test_coverage_report_fixture_empty_fasta_file(self, tmpdir):
tmpdir = str(tmpdir)
coverage_file = copy_fixture('SRP0741/SRP074153/SRR6257/SRR6257420/megahit/001/coverage.tab',
tmpdir + 'tmp.tab')
contig_file = write_empty_file(tmpdir + 'contigs.fasta')
output_file = write_empty_file(tmpdir + 'output.json')
open(coverage_file, 'a').close()
args = gen_stats_report.parse_args(
['106000', contig_file, coverage_file, output_file, '500', 'metaspades'])
coverage = gen_stats_report.calc_coverage(args)
assert coverage == 14.2
def test_main_megahit(self, tmpdir):
tmpdir = str(tmpdir)
contig_file = copy_fixture('SRP0741/SRP074153/SRR6257/SRR6257420/megahit/001/final.contigs.fa',
tmpdir + 'contigs.fasta')
coverage_file = copy_fixture('SRP0741/SRP074153/SRR6257/SRR6257420/megahit/001/coverage.tab',
tmpdir + 'coverage.tab')
output_file = write_empty_file(tmpdir + 'output.json')
base_count = 106000
args = gen_stats_report.parse_args([str(base_count), contig_file, coverage_file, output_file, '0', 'megahit'])
try:
gen_stats_report.main(args)
except SystemExit:
pass
expected_report = {
'Base count': base_count,
'Coverage': 14.2,
'Min length 1000 bp': {'num_contigs': 1, 'total_base_pairs': 2473},
'Min length 10000 bp': {'num_contigs': 0, 'total_base_pairs': 0},
'Min length 50000 bp': {'num_contigs': 0, 'total_base_pairs': 0},
'num_contigs': 22,
'total_assembled_pairs': 11716,
'largest_contig': 2473,
'n50': 9,
'l50': 14
}
with open(output_file) as output:
report = json.load(output)
assert expected_report == report
def test_main_metaspades(self, tmpdir):
tmpdir = str(tmpdir)
contig_file = copy_fixture('ERP0102/ERP010229/ERR8665/ERR866589/metaspades/001/contigs.fasta',
tmpdir + 'contigs.fasta')
coverage_file = copy_fixture('ERP0102/ERP010229/ERR8665/ERR866589/metaspades/001/coverage.tab',
tmpdir + 'coverage.tab')
output_file = write_empty_file(tmpdir + 'output.json')
base_count = 106000
args = gen_stats_report.parse_args(
[str(base_count), contig_file, coverage_file, output_file, '0', 'metaspades'])
try:
gen_stats_report.main(args)
except SystemExit:
pass
expected_report = {
'Base count': base_count,
'Coverage': 0.01,
'Min length 1000 bp': {'num_contigs': 0, 'total_base_pairs': 0},
'Min length 10000 bp': {'num_contigs': 0, 'total_base_pairs': 0},
'Min length 50000 bp': {'num_contigs': 0, 'total_base_pairs': 0},
'num_contigs': 5,
'total_assembled_pairs': 262 + 245 + 116 + 87 + 60,
'largest_contig': 262,
'n50': 2,
'l50': 4
}
with open(output_file) as output:
report = json.load(output)
assert expected_report == report
def test_stats_empty_fasta(self, tmpdir):
tmpdir = str(tmpdir)
contig_file = write_empty_file(tmpdir + 'contigs.fasta')
with open(contig_file) as f:
fstats = gen_stats_report.FastaStats(f, 500, 'metaspades')
fstats.parse_file()
assert fstats.get_largest_contig() == 0
assert fstats.get_n50() == 0
assert fstats.get_l50() == 0
assert fstats.get_total_pairs() == 0
assert fstats.get_filtered_stats(100) == {'num_contigs': 0, 'total_base_pairs': 0}
def test_raises_error_on_invalid_basecount(self, tmpdir):
tmpdir = str(tmpdir)
contig_file = copy_fixture('SRP0741/SRP074153/SRR6257/SRR6257420/megahit/001/final.contigs.fa',
tmpdir + 'contigs.fasta')
coverage_file = copy_fixture('SRP0741/SRP074153/SRR6257/SRR6257420/megahit/001/coverage.tab',
tmpdir + 'coverage.tab')
output_file = write_empty_file(tmpdir + 'output.json')
with pytest.raises(ValueError) as exc:
args = gen_stats_report.parse_args(['0', contig_file, coverage_file, output_file, '0', 'metaspades'])
gen_stats_report.main(args)
# Assert error comes from coverage file message, not fasta parsing error
assert 'Base count (0) cannot be <= 0.' in str(exc)