def test_calculate_stats():
'It tests the calculate stat function'
in_fhands = []
for val in range(1, 6):
fhand = open(join(TEST_DATA_DIR, 'pairend{0}.sfastq'.format(val)))
in_fhands.append(fhand)
seqs = read_seqs(in_fhands, prefered_seq_classes=[SEQRECORD])
results = calculate_sequence_stats(seqs, nxs=[50])
assert 'maximum: 4' in results['length']
assert 'N50' in results['length']
assert '1:30.0,30.0,30.0,30.0,30.0 <[|]>' in results['qual_boxplot']
assert '[30 , 31[ (96): **********' in results['quality']
assert 'Q30: 100.0' in results['quality']
assert '0 (A: 1.00, C: 0.00, G: 0.00, T: 0.00' in results['nucl_freq']
assert results['kmer'] == ''
infhands = [open(join(TEST_DATA_DIR, 'arabidopsis_genes'))]
seqs = list(read_seqs(infhands, prefered_seq_classes=[SEQRECORD]))
kmers = calculate_sequence_stats(seqs)['kmer']
assert not 'Kmer distribution' in kmers
kmers = calculate_sequence_stats(seqs, kmer_size=3)['kmer']
assert 'Kmer distribution' in kmers
assert 'TCT: 167' in kmers
# dust
dust = calculate_sequence_stats(seqs)['dustscore']
assert not dust
dust = calculate_sequence_stats(seqs, do_dust_stats=True)['dustscore']
assert 'average: 1.83\nvariance: 0.14\nnum. seqs.: 6\n' in dust
assert '% above 7 (low complexity): 0.00' in dust
def test_calculate_stats():
'It tests the calculate stat function'
in_fhands = []
for val in range(1, 6):
fhand = open(join(TEST_DATA_DIR, 'pairend{0}.sfastq'.format(val)))
in_fhands.append(fhand)
seqs = read_seqrecords(in_fhands, file_format='fastq')
(lengths_srt, qual_str, freq_str,
qual_boxplot, kmers) = calculate_sequence_stats(seqs)
assert 'maximum: 4' in lengths_srt
assert 'Q30: 100.0' in qual_str
assert '1:30.0,30.0,30.0,30.0,30.0 <[|]>' in qual_boxplot
assert '[30 , 31[ (96): **********' in qual_str
assert '0 (A: 1.00, C: 0.00, G: 0.00, T: 0.00, N: 0.00) |' in freq_str
assert kmers == ''
infhands = [open(join(TEST_DATA_DIR, 'arabidopsis_genes'))]
seqs = read_seqrecords(infhands, file_format='fasta')
kmers = calculate_sequence_stats(seqs)[-1]
assert not 'Kmer distribution' in kmers
infhands = [open(join(TEST_DATA_DIR, 'arabidopsis_genes'))]
seqs = read_seqrecords(infhands, file_format='fasta')
kmers = calculate_sequence_stats(seqs, kmer_size=3)[-1]
assert 'Kmer distribution' in kmers
assert 'TCT: 167' in kmers
def test_calculate_stats():
'It tests the calculate stat function'
in_fhands = []
for val in range(1, 6):
fhand = open(join(TEST_DATA_DIR, 'pairend{0}.sfastq'.format(val)))
in_fhands.append(fhand)
seqs = read_seqs(in_fhands, prefered_seq_classes=[SEQRECORD])
results = calculate_sequence_stats(seqs, nxs=[50])
assert 'maximum: 4' in results['length']
assert 'N50' in results['length']
assert '1:30.0,30.0,30.0,30.0,30.0 <[|]>' in results['qual_boxplot']
assert '[30 , 31[ (96): **********' in results['quality']
assert 'Q30: 100.0' in results['quality']
assert '0 (A: 1.00, C: 0.00, G: 0.00, T: 0.00' in results['nucl_freq']
assert results['kmer'] == ''
infhands = [open(join(TEST_DATA_DIR, 'arabidopsis_genes'))]
seqs = list(read_seqs(infhands, prefered_seq_classes=[SEQRECORD]))
kmers = calculate_sequence_stats(seqs)['kmer']
assert not 'Kmer distribution' in kmers
kmers = calculate_sequence_stats(seqs, kmer_size=3)['kmer']
assert 'Kmer distribution' in kmers
assert 'TCT: 167' in kmers
# dust
dust = calculate_sequence_stats(seqs)['dustscore']
assert not dust
dust = calculate_sequence_stats(seqs, do_dust_stats=True)['dustscore']
assert 'average: 1.83\nvariance: 0.14\nnum. seqs.: 6\n' in dust
assert '% above 7 (low complexity): 0.00' in dust
def test_calculate_stats_seqitems():
'It tests the calculate stat function with seqitems'
in_fhands = []
for val in range(1, 6):
fhand = open(join(TEST_DATA_DIR, 'pairend{0}.sfastq'.format(val)))
in_fhands.append(fhand)
seqs = read_seqs(in_fhands, prefered_seq_classes=[SEQITEM])
results = calculate_sequence_stats(seqs, nxs=[50])
assert 'maximum: 4' in results['length']
assert 'N50' in results['length']
assert '1:30.0,30.0,30.0,30.0,30.0 <[|]>' in results['qual_boxplot']
assert '[30 , 31[ (96): **********' in results['quality']
assert 'Q30: 100.0' in results['quality']
assert '0 (A: 1.00, C: 0.00, G: 0.00, T: 0.00' in results['nucl_freq']
assert results['kmer'] == ''
def test_calculate_stats_seqitems():
'It tests the calculate stat function with seqitems'
in_fhands = []
for val in range(1, 6):
fhand = open(join(TEST_DATA_DIR, 'pairend{0}.sfastq'.format(val)))
in_fhands.append(fhand)
seqs = read_seqs(in_fhands, prefered_seq_classes=[SEQITEM])
results = calculate_sequence_stats(seqs, nxs=[50])
assert 'maximum: 4' in results['length']
assert 'N50' in results['length']
assert '1:30.0,30.0,30.0,30.0,30.0 <[|]>' in results['qual_boxplot']
assert '[30 , 31[ (96): **********' in results['quality']
assert 'Q30: 100.0' in results['quality']
assert '0 (A: 1.00, C: 0.00, G: 0.00, T: 0.00' in results['nucl_freq']
assert results['kmer'] == ''