def test_filter_n(self):
ht = khmer.new_hashtable(10, 4**10)
filename = utils.get_test_data('simple_2.fa')
outname = utils.get_temp_filename('test_filter.out')
(total_reads, n_consumed) = ht.consume_fasta(filename)
assert total_reads == 4, total_reads
assert n_consumed == 63, n_consumed
(total_reads, n_seq_kept) = khmer.filter_fasta_file_any(ht, filename,
total_reads,
outname, 1)
assert n_seq_kept == 3, n_seq_kept
names = load_fa_seq_names(outname)
assert names == ['1', '2', '3']
def test_filter_n(self):
ht = khmer.new_hashtable(10, 4**10)
filename = utils.get_test_data('simple_2.fa')
outname = utils.get_temp_filename('test_filter.out')
(total_reads, n_consumed) = ht.consume_fasta(filename)
assert total_reads == 4, total_reads
assert n_consumed == 63, n_consumed
(total_reads,
n_seq_kept) = khmer.filter_fasta_file_any(ht, filename, total_reads,
outname, 1)
assert n_seq_kept == 3, n_seq_kept
names = load_fa_seq_names(outname)
assert names == ['1', '2', '3']
def test_filter(self):
ht = khmer.new_hashtable(10, 4**10)
filename = os.path.join(thisdir, 'test_data/simple_1.fa')
outname = os.path.join(self.tempdir, 'test_filter.out')
(total_reads, n_consumed) = ht.consume_fasta(filename)
assert total_reads == 3, total_reads
assert n_consumed == 63, n_consumed
(total_reads, n_seq_kept) = khmer.filter_fasta_file_any(ht, filename,
total_reads,
outname, 2)
assert n_seq_kept == 2, n_seq_kept
names = load_fa_seq_names(outname)
assert names == ['1', '2']
