def test_compute_n50_from_file(self): """ Test getting N50 from file """ with self.assertRaises(IOError): get_fasta_readlengths('what.ever') fasta = os.path.join( ROOT_DATA_DIR, 'polished_assembly', 'polished_assembly.fasta.gz') self.assertEqual( 33586, compute_n50_from_file(fasta) )
def test_compute_n50_from_file(self): """ Test getting N50 from file """ with self.assertRaises(IOError): get_fasta_readlengths('what.ever') fasta = os.path.join(ROOT_DATA_DIR, 'polished_assembly', 'polished_assembly.fasta.gz') self.assertEqual(33586, compute_n50_from_file(fasta))
def test_get_fasta_readlengths(self): """ Test getting num reads and total readlength """ with self.assertRaises(IOError): get_fasta_readlengths('what.ever') fasta = os.path.join( ROOT_DATA_DIR, 'polished_assembly', 'polished_assembly.fasta.gz') l = get_fasta_readlengths(fasta) self.assertEqual( 2, len(l) ) self.assertEqual( 47938, sum(l) )
def test_get_fasta_readlengths(self): """ Test getting num reads and total readlength """ with self.assertRaises(IOError): get_fasta_readlengths('what.ever') fasta = os.path.join(ROOT_DATA_DIR, 'polished_assembly', 'polished_assembly.fasta.gz') l = get_fasta_readlengths(fasta) self.assertEqual(2, len(l)) self.assertEqual(47938, sum(l))
def test_compute_n50_from_readlenths(self): """ Test getting N50 from length list """ fasta = os.path.join( ROOT_DATA_DIR, 'polished_assembly', 'polished_assembly.fasta.gz') l = get_fasta_readlengths(fasta) self.assertEqual( 33586, compute_n50(l) )
def test_compute_n50_from_readlenths(self): """ Test getting N50 from length list """ fasta = os.path.join(ROOT_DATA_DIR, 'polished_assembly', 'polished_assembly.fasta.gz') l = get_fasta_readlengths(fasta) self.assertEqual(33586, compute_n50(l))
def from_file(file_name): # nreads, total = _compute_values(file_name) read_lens = get_fasta_readlengths(file_name) nreads = len(read_lens) total = sum(read_lens) return FastaContainer(nreads, total, file_name)