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_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_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)
def test_compress_file_should_make_output_dir(self, tmpdir):
tmpdir = str(tmpdir)
fasta_file = copy_fixture('SRP0741/SRP074153/SRR6257/SRR6257420/megahit/001/final.contigs.fa',
tmpdir + '/contigs.fasta')
out_file = os.path.join(os.path.dirname(fasta_file), 'extra_dir', os.path.basename(fasta_file) + '.gzip')
compress_file(fasta_file, out_file)
assert os.path.exists(out_file)
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_write_md5_should_output_md5file(self, tmpdir):
tmpdir = str(tmpdir)
fasta_file = copy_fixture('SRP0741/SRP074153/SRR6257/SRR6257420/megahit/001/final.contigs.fa',
tmpdir + '/contigs.fasta')
write_md5(fasta_file)
with open(fasta_file + '.md5') as f:
md5 = f.read()
assert md5 == 'dc94b51a736f6a43e146f1c1133d7aab'
def test_compress_file_should_be_gzip(self, tmpdir):
tmpdir = str(tmpdir)
fasta_file = copy_fixture('SRP0741/SRP074153/SRR6257/SRR6257420/megahit/001/final.contigs.fa',
tmpdir + '/contigs.fasta')
out_file = fasta_file + '.gzip'
compress_file(fasta_file, out_file)
out_file_content = gzip.open(out_file, 'rb').read()
assert open(fasta_file, 'rb').read() == out_file_content
def test_compress_file_should_be_smaller(self, tmpdir):
tmpdir = str(tmpdir)
fasta_file = copy_fixture('SRP0741/SRP074153/SRR6257/SRR6257420/megahit/001/final.contigs.fa',
tmpdir + '/contigs.fasta')
out_file = fasta_file + '.gzip'
compress_file(fasta_file, out_file)
assert os.path.exists(out_file)
assert os.stat(fasta_file).st_size > os.stat(out_file).st_size
def test_trim_megahit_assembler(self, tmpdir):
tmpdir = str(tmpdir)
assembler = 'megahit'
min_contig_length = 400
fasta_file = copy_fixture('SRP0741/SRP074153/SRR6257/SRR6257420/megahit/001/final.contigs.fa',
tmpdir + '/contigs.fasta')
output_file = tmpdir + 'output.fasta'
trim_and_validate_against_trim(fasta_file, output_file, min_contig_length, assembler)
def test_trim_metaspades_assembler(self, tmpdir):
tmpdir = str(tmpdir)
assembler = 'metaspades'
min_contig_length = 200
fasta_file = copy_fixture('ERP0102/ERP010229/ERR8665/ERR866589/metaspades/001/contigs.fasta',
tmpdir + '/contigs.fasta')
output_file = tmpdir + 'output.fasta'
trim_and_validate_against_trim(fasta_file, output_file, min_contig_length, assembler)
def test_main_should_duplicate_fasta_if_no_trimming_required(self, tmpdir):
tmpdir = str(tmpdir)
fasta_file = copy_fixture('SRP0741/SRP074153/SRR6257/SRR6257420/megahit/001/final.contigs.fa',
tmpdir + '/contigs.fasta')
output_name = os.path.join(tmpdir, 'output')
args = parse_args([fasta_file, '0', output_name, 'megahit'])
fasta_trim_main(args)
assert open(fasta_file, 'rb').read() == open(output_name + '.fasta', 'rb').read()
def test_main_should_output_files(self, tmpdir):
tmpdir = str(tmpdir)
fasta_file = copy_fixture('SRP0741/SRP074153/SRR6257/SRR6257420/megahit/001/final.contigs.fa',
tmpdir + '/contigs.fasta')
output_name = os.path.join(tmpdir, 'output')
args = parse_args([fasta_file, '500', output_name, 'megahit'])
fasta_trim_main(args)
os.path.exists(tmpdir + '.contigs.fasta')
os.path.exists(tmpdir + '.contigs.fasta.gz')
os.path.exists(tmpdir + '.contigs.fasta.gz.md5')
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_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