def test_missing_inputs(self):
magellan.bowtie2_build_index(
os.path.join(_sample_data_dir, 'sample_bac_genome_short.fa'),
os.path.join(_sample_data_dir, 'test_index'))
with self.assertRaises(RuntimeError):
magellan.bowtie2_map(
os.path.join(_sample_data_dir, 'madeup.fastq'),
os.path.join(_sample_data_dir, 'test_index'),
os.path.join(_sample_data_dir, 'sample_reads_for_mapper.sam'),
os.path.join(_sample_data_dir, 'sample_reads_for_mapper.log'))
with self.assertRaises(RuntimeError):
magellan.bowtie2_map(
os.path.join(_sample_data_dir,
'sample_reads_for_mapper.fastq'),
os.path.join(_sample_data_dir, 'madeup_index'),
os.path.join(_sample_data_dir, 'sample_reads_for_mapper.sam'),
os.path.join(_sample_data_dir, 'sample_reads_for_mapper.log'))
index_files = glob.glob(os.path.join(_sample_data_dir, 'test_index.*'))
for i in index_files:
os.remove(i)
s = os.path.join(_sample_data_dir, 'sample_reads_for_mapper.sam')
if os.path.isfile(s):
os.remove(s)
l = os.path.join(_sample_data_dir, 'sample_reads_for_mapper.sam')
if os.path.isfile(l):
os.remove(l)
def setUpClass(cls):
magellan.bowtie2_build_index(
os.path.join(_sample_data_dir, 'sample_bac_genome_short.fa'),
os.path.join(_sample_data_dir, 'test_index'))
magellan.bowtie2_map(
os.path.join(_sample_data_dir, 'sample_reads_for_mapper.fastq'),
os.path.join(_sample_data_dir, 'test_index'),
os.path.join(_sample_data_dir, 'sample_reads_for_mapper.sam'),
os.path.join(_sample_data_dir, 'sample_reads_for_mapper.log'))
def test_basic(self):
magellan.bowtie2_build_index(
os.path.join(_sample_data_dir, 'sample_bac_genome_short.fa'),
os.path.join(_sample_data_dir, 'test_index'))
index_files = glob.glob(os.path.join(_sample_data_dir, 'test_index.*'))
for i in index_files:
os.remove(i)
magellan.bowtie2_build_index(os.path.join(
_sample_data_dir, 'sample_bac_genome_short.fa'),
os.path.join(_sample_data_dir,
'test_index_offrate'),
offrate=2)
offrate_index_files = glob.glob(
os.path.join(_sample_data_dir, 'test_index_offrate.*'))
for i in offrate_index_files:
os.remove(i)
def test_basic(self):
magellan.bowtie2_build_index(
os.path.join(_sample_data_dir, 'sample_bac_genome_short.fa'),
os.path.join(_sample_data_dir, 'test_index'))
magellan.bowtie2_map(
os.path.join(_sample_data_dir, 'sample_reads_for_mapper.fastq'),
os.path.join(_sample_data_dir, 'test_index'),
os.path.join(_sample_data_dir, 'sample_reads_for_mapper.sam'),
os.path.join(_sample_data_dir, 'sample_reads_for_mapper.log'))
index_files = glob.glob(os.path.join(_sample_data_dir, 'test_index'))
for i in index_files:
os.remove(i)
os.remove(os.path.join(_sample_data_dir,
'sample_reads_for_mapper.sam'))
os.remove(os.path.join(_sample_data_dir,
'sample_reads_for_mapper.log'))
def test_missing_fasta(self):
with self.assertRaises(RuntimeError):
magellan.bowtie2_build_index(
os.path.join(_sample_data_dir, 'madeup.fa'),
os.path.join(_sample_data_dir, 'test_index'))