#!/usr/bin/env python3
from sod import sod
read_len = 250
records = sod.simulate_reads('tests/hxb2.fasta', n_reads=1000, read_len=read_len,
sub_rate=0.1, ins_rate=0.1, del_rate=0.1,
fastq=False, uppercase=False)
def test_simulate():
assert records
def test_read_lens():
for record in records:
assert len(record.seq) == read_len
def test_fastq():
records_mixedcase = sod.simulate_reads('tests/hxb2.fasta', n_reads=1000,
read_len=read_len, sub_rate=0.1,
ins_rate=0.1, del_rate=0.1,
fastq=True, uppercase=False)
records_uppercase = sod.simulate_reads('tests/hxb2.fasta', n_reads=1000,
read_len=read_len, sub_rate=0.1,
ins_rate=0.1, del_rate=0.1,
fastq=True, uppercase=True)
quality_mixedcase = records_mixedcase[0].letter_annotations['phred_quality']
quality_uppercase = records_uppercase[0].letter_annotations['phred_quality']
def test_fastq():
records_mixedcase = sod.simulate_reads('tests/hxb2.fasta', n_reads=1000,
read_len=read_len, sub_rate=0.1,
ins_rate=0.1, del_rate=0.1,
fastq=True, uppercase=False)
records_uppercase = sod.simulate_reads('tests/hxb2.fasta', n_reads=1000,
read_len=read_len, sub_rate=0.1,
ins_rate=0.1, del_rate=0.1,
fastq=True, uppercase=True)
quality_mixedcase = records_mixedcase[0].letter_annotations['phred_quality']
quality_uppercase = records_uppercase[0].letter_annotations['phred_quality']
