def test_stats_valid_megahit_fasta_with_contig_filtering(self, tmpdir):
tmpdir = str(tmpdir)
contig_file = copy_fixture('SRP0741/SRP074153/SRR6257/SRR6257420/megahit/001/final.contigs.fa',
tmpdir + 'contigs.fasta')
with open(contig_file) as f:
fstats = gen_stats_report.FastaStats(f, 700, 'megahit')
fstats.parse_file()
contig_lengths = 2473 + 767 + 730
expected_report = {
'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': 3,
'total_assembled_pairs': contig_lengths,
'largest_contig': 2473,
'n50': 1,
'l50': 3
}
assert fstats.get_largest_contig() == expected_report['largest_contig']
assert fstats.get_n50() == expected_report['n50']
assert fstats.get_l50() == expected_report['l50']
assert fstats.get_total_pairs(), expected_report['total_assembled_pairs']
assert fstats.get_filtered_stats(2000) == {'num_contigs': 1, 'total_base_pairs': 2473}
assert fstats.gen_report() == expected_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_stats_valid_metaspades_fasta_with_contig_filtering(self, tmpdir):
tmpdir = str(tmpdir)
contig_file = copy_fixture('ERP0102/ERP010229/ERR8665/ERR866589/metaspades/001/contigs.fasta',
tmpdir + 'contigs.fasta')
with open(contig_file) as f:
fstats = gen_stats_report.FastaStats(f, 100, 'metaspades')
fstats.parse_file()
expected_report = {
'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': 3,
'total_assembled_pairs': 262 + 245 + 116,
'largest_contig': 262,
'n50': 2,
'l50': 2
}
assert fstats.get_largest_contig() == expected_report['largest_contig']
assert fstats.get_n50() == expected_report['n50']
assert fstats.get_l50() == expected_report['l50']
assert fstats.get_total_pairs() == expected_report['total_assembled_pairs']
assert fstats.get_filtered_stats(100) == {'num_contigs': 3, 'total_base_pairs': 262 + 245 + 116}
assert fstats.gen_report() == expected_report
def test_unsupported_assemblers(self):
unsupported = ['minia', 'invalid_assembler']
for assembler in unsupported:
with pytest.raises(ValueError):
gen_stats_report.FastaStats('contigs.fasta', 500, assembler)
def test_supported_assemblers(self):
supported = ['metaspades', 'spades', 'megahit']
for assembler in supported:
fstats = gen_stats_report.FastaStats('contigs.fasta', 500, assembler)
assert fstats.assembler == assembler