def test_save_no_load(self): filename = utils.get_temp_filename('tst') rt = self.rt rt.set(0, True) rt.set(1, False) rt.set(2, True) rt.set(3, False) rt.set(4, True) rt.save(filename) rt2 = khmer.new_readmask(READTABLE_SIZE) # no load! try: for i in range(5): if rt.get(i) != rt2.get(i): raise Exception # supposed to happen; no load. assert 0 except AssertionError: raise except Exception: pass
def test_raise_in_readmask_filter_fasta_file(): readmask = khmer.new_readmask(N_READS) try: readmask.filter_fasta_file(reads_filename, "tst", callback_raise) assert 0 except GoodException: pass except: raise
def test_merge_3(self): rt = self.rt rt2 = khmer.new_readmask(READTABLE_SIZE) rt.set(0, False) rt2.set(0, True) rt.merge(rt2) v = rt.get(0) assert not v, v
def test_readmask_1(self): filename = utils.get_test_data('simple_2.fa') outname = utils.get_temp_filename('test_filter.out') readmask = khmer.new_readmask(4) readmask.set(1, False) readmask.set(2, False) readmask.set(3, False) readmask.filter_fasta_file(filename, outname) names = load_fa_seq_names(outname) assert names == ['1'], names
def test_raise_in_readmask_filter_fasta_file(): return # @@CTB fix readmask = khmer.new_readmask(N_READS) tstfile = utils.get_temp_filename('tst') try: readmask.filter_fasta_file(reads_filename, tstfile, callback_raise) assert 0 except GoodException: pass except: raise
def test_readmask_1(self): filename = os.path.join(thisdir, 'test_data/simple_2.fa') outname = os.path.join(self.tempdir, 'test_filter.out') readmask = khmer.new_readmask(4) readmask.set(1, False) readmask.set(2, False) readmask.set(3, False) readmask.filter_fasta_file(filename, outname) names = load_fa_seq_names(outname) assert names == ['1'], names
def test_saveload(self): rt = self.rt rt.set(0, True) rt.set(1, False) rt.set(2, True) rt.set(3, False) rt.set(4, True) rt.save(self.filename) rt2 = khmer.new_readmask(0) rt2.load(self.filename) for i in range(5): assert rt.get(i) == rt2.get(i), i
def test_consume_update_readmask(self): ht = khmer.new_hashtable(10, 4**10) filename = os.path.join(thisdir, 'test_data/simple_2.fa') outname = os.path.join(self.tempdir, 'test_filter.out') readmask = khmer.new_readmask(4) # sequence #4 (index 3) is bad; the new readmask should have that. (total_reads, n_consumed) = ht.consume_fasta(filename, 0, 0, readmask, True) assert total_reads == 4, total_reads assert n_consumed == 63, n_consumed assert readmask.get(0) assert readmask.get(1) assert readmask.get(2) assert not readmask.get(3)
def test_consume_no_update_readmask(self): ht = khmer.new_hashtable(10, 4**10) filename = utils.get_test_data('simple_2.fa') outname = utils.get_temp_filename('test_filter.out') readmask = khmer.new_readmask(4) # sequence #4 (index 3) is bad; the new readmask should NOT have that. (total_reads, n_consumed) = ht.consume_fasta(filename, 0, 0, readmask, False) assert total_reads == 4, total_reads assert n_consumed == 63, n_consumed assert readmask.get(0) assert readmask.get(1) assert readmask.get(2) assert readmask.get(3) # NOT updated
def test_saveload(self): filename = utils.get_temp_filename('tst') rt = self.rt rt.set(0, True) rt.set(1, False) rt.set(2, True) rt.set(3, False) rt.set(4, True) rt.save(filename) rt2 = khmer.new_readmask(0) rt2.load(filename) for i in range(5): assert rt.get(i) == rt2.get(i), i
#! /usr/bin/env python import sys import khmer sequence_file = sys.argv[1] readmask_file = sys.argv[2] output_file = sys.argv[3] r = khmer.new_readmask(0) r.load(readmask_file) r.filter_fasta_file(sequence_file, output_file)
def __init__(self): self.rt = khmer.new_readmask(READTABLE_SIZE)
def __init__(self): self.rt = khmer.new_readmask(READTABLE_SIZE) self.tempdir = tempfile.mkdtemp() self.filename = os.path.join(self.tempdir, 'tst')