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_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_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_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 = 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_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_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
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')
def __init__(self):
self.rt = khmer.new_readmask(READTABLE_SIZE)
