#!/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']