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)