def test_small_input():
err_mod = kde.KDErrorModel('data/ecoli.npz')
ref_genome = SeqRecord(
Seq(str('AAAAACCCCC'),
IUPAC.unambiguous_dna
),
id='my_genome',
description='test genome'
)
generator.simulate_read(ref_genome, err_mod, 1, 0)
def test_kde_short():
if sys.version_info > (3, ):
random.seed(42)
np.random.seed(42)
err_mod = kde.KDErrorModel('data/ecoli.npz')
ref_genome = SeqRecord(Seq(str('AAACC' * 100), IUPAC.unambiguous_dna),
id='my_genome',
description='test genome')
read_tuple = generator.simulate_read(ref_genome, err_mod, 1)
big_read = ''.join(str(read_tuple[0].seq) + str(read_tuple[1].seq))
assert big_read == 'ACCAAACCAAACCAAACCAAGGTTTGGTTTGGTTTGGTGT'
def test_basic():
if sys.version_info > (3, ):
random.seed(42)
np.random.seed(42)
err_mod = basic.BasicErrorModel()
ref_genome = SeqRecord(Seq(str('AAAAACCCCC' * 100),
IUPAC.unambiguous_dna),
id='my_genome',
description='test genome')
read_tuple = generator.simulate_read(ref_genome, err_mod, 1)
big_read = ''.join(str(read_tuple[0].seq) + str(read_tuple[1].seq))
assert big_read[-15:] == 'TTTTGGGGGTTTTTG'
sigma=community['stdev_log_abund'])
community['sim_abund'].to_csv(abund_path, sep='\t')
replicon['sim_copies'] = (replicon['genome_id'].map(community['sim_abund']) *
replicon['replicon_type']
.map({'chromosome': 1,
'plasmid': PLASMID_MULTI})
.fillna(1))
replicon['sim_nucleotides'] = replicon['sim_copies'] * replicon['size']
replicon['sim_pread'] = (replicon['sim_nucleotides'] /
replicon['sim_nucleotides'].sum())
replicon['sim_nreads'] = np.random.multinomial(nreads, replicon['sim_pread'])
print(replicon[['genbank_id', 'size', 'sim_nreads']], file=sys.stderr)
print('Simulating metagenome reads.', file=sys.stderr)
model_path = os.path.join(iss.__path__[0], 'profiles', ERR_MODEL_NAME)
err_model = KDErrorModel(model_path)
with open(r1_path, 'w') as handle1, open(r2_path, 'w') as handle2:
reads_so_far = 0
for genome_id, g in replicon.groupby('genome_id'):
print(f'Simulating reads for genome {genome_id}', file=sys.stderr)
genome_path = os.path.join(genome_dir, genome_id + '.fn')
seqs = seq_file_index(genome_path, 'fasta')
for replicon_id, r in g.iterrows():
print(f'Simulating reads for replicon {replicon_id}', file=sys.stderr)
record = seqs[r.genbank_id]
for i in tqdm(range(r.sim_nreads), initial=reads_so_far, total=nreads):
paired_reads = simulate_read(record, err_model, i)
write_seq(paired_reads[0], handle1, 'fastq-sanger')
write_seq(paired_reads[1], handle2, 'fastq-sanger')
reads_so_far += r.sim_nreads