def test_indexstar_and_mapstar(self):
genome = make_fasta_file(num_sequences=2, seq_len=1000, rnd_seed=0)
fastq = make_fastq_file(genome=genome, rnd_seed=0)
command_basic = [
'iCount',
'indexstar',
genome,
self.dir,
'-S',
'40', # Supress lower than ERROR messages.
]
self.assertEqual(subprocess.call(command_basic), 0)
command_basic = [
'iCount',
'mapstar',
fastq,
self.dir,
self.dir2,
'-S',
'40', # Supress lower than ERROR messages.
]
self.assertEqual(subprocess.call(command_basic), 0)
def test_cutadapt(self):
adapter = 'CCCCCCCCC'
fastq = make_fastq_file(adapter=adapter,
out_file=get_temp_file_name(extension='fastq'),
rnd_seed=0)
command_basic = [
'iCount',
'cutadapt',
fastq,
self.tmp1,
adapter,
'-S',
'40', # Supress lower than ERROR messages.
]
command_full = [
'iCount',
'cutadapt',
fastq,
self.tmp1,
adapter,
'--qual_trim',
'20',
'--minimum_length',
'15',
'-S',
'40', # Supress lower than ERROR messages.
]
self.assertEqual(subprocess.call(command_basic), 0)
self.assertEqual(subprocess.call(command_full), 0)
def setUp(self):
self.adapter = 'AAAATTTTCCCCGGGG'
self.reads = make_fastq_file(
adapter=self.adapter,
num_sequences=100,
out_file=get_temp_file_name(extension='fastq'))
self.tmp = get_temp_file_name(extension='fastq')
warnings.simplefilter("ignore", ResourceWarning)
def setUp(self):
self.dir = get_temp_dir()
self.adapter = 'CCCCCCCCC'
self.barcodes = [
'NNNGGTTNN',
'NNNTTGTNN',
'NNNCAATNN',
'NNNACCTNN',
'NNNGGCGNN',
]
self.reads = make_fastq_file(barcodes=self.barcodes,
adapter=self.adapter)
warnings.simplefilter("ignore", ResourceWarning)
def test_demultiplex(self):
barcodes = [
'NNNTTGTNN',
'NNNGGTTNN',
'NNNGGCGNN',
]
bar1, bar2, bar3 = barcodes
adapter = 'CCCCCCCCC'
fastq = make_fastq_file(barcodes=barcodes, adapter=adapter, rnd_seed=0)
command_basic = [
'iCount',
'demultiplex',
fastq,
adapter,
bar1,
bar2,
bar3,
'--mismatches',
'2',
'--out_dir',
self.dir, # put files in tmpdir, to not pollute cwd.
'-S',
'40', # Supress lower than ERROR messages.
]
command_full = [
'iCount',
'demultiplex',
fastq,
adapter,
bar1,
bar2,
bar3,
'--mismatches',
'2',
'--minimum_length',
'15',
'--prefix',
'demux',
'--out_dir',
self.dir,
'-S',
'40', # Supress lower than ERROR messages.
]
self.assertEqual(subprocess.call(command_basic), 0)
self.assertEqual(subprocess.call(command_full), 0)
def setUp(self):
self.dir = get_temp_dir()
self.index_dir = get_temp_dir()
self.genome = make_fasta_file(num_sequences=2, seq_len=1000)
self.reads = make_fastq_file(genome=self.genome)
self.annotation = make_file_from_list([
['1', '.', 'gene', '10', '20', '.', '+', '.', 'gene_id "A";'],
[
'1', '.', 'transcript', '10', '20', '.', '+', '.',
'gene_id "A"; transcript_id "AA";'
],
[
'1', '.', 'exon', '10', '20', '.', '+', '.',
'gene_id "A"; transcript_id "AA"; exon_number "1";'
],
])
warnings.simplefilter("ignore", ResourceWarning)
def test_indexstar_and_mapstar_full(self):
genome = make_fasta_file(num_sequences=2, seq_len=1000, rnd_seed=0)
fastq = make_fastq_file(genome=genome, rnd_seed=0)
command_full = [
'iCount',
'indexstar',
genome,
self.dir,
'--annotation',
self.gtf,
'--overhang',
'100',
'--overhang_min',
'8',
'--threads',
'1',
'-S',
'40', # Supress lower than ERROR messages.
]
self.assertEqual(subprocess.call(command_full), 0)
command_full = [
'iCount',
'mapstar',
fastq,
self.dir,
self.dir2,
'--annotation',
self.gtf,
'--multimax',
'50',
'--mismatches',
'2',
'--threads',
'1',
'-S',
'40', # Supress lower than ERROR messages.
]
self.assertEqual(subprocess.call(command_full), 0)
