def test_filter_limit_n(self):
ht = khmer.new_hashtable(4, 4**4)
filename = utils.get_test_data('simple_3.fa')
outname = utils.get_temp_filename('test_filter.out')
(total_reads, n_consumed) = ht.consume_fasta(filename)
assert total_reads == 2, total_reads
(total_reads, n_seq_kept) = \
khmer.filter_fasta_file_limit_n(ht, filename,
total_reads,
outname, 2,
7)
assert total_reads == 2
assert n_seq_kept == 1
(total_reads, n_seq_kept) = \
khmer.filter_fasta_file_limit_n(ht, filename,
total_reads,
outname, 2,
4)
assert total_reads == 2
assert n_seq_kept == 2
def test_filter_limit_n(self):
ht = khmer.new_hashtable(4, 4**4)
filename = utils.get_test_data('simple_3.fa')
outname = utils.get_temp_filename('test_filter.out')
(total_reads, n_consumed) = ht.consume_fasta(filename)
assert total_reads == 2, total_reads
(total_reads, n_seq_kept) = \
khmer.filter_fasta_file_limit_n(ht, filename,
total_reads,
outname, 2,
7)
assert total_reads == 2
assert n_seq_kept == 1
(total_reads, n_seq_kept) = \
khmer.filter_fasta_file_limit_n(ht, filename,
total_reads,
outname, 2,
4)
assert total_reads == 2
assert n_seq_kept == 2
def test_filter_limit_n(self):
ht = khmer.new_hashtable(4, 4**4)
filename = os.path.join(thisdir, 'test-data/simple_3.fa')
outname = os.path.join(self.tempdir, 'test_filter.out')
(total_reads, n_consumed) = ht.consume_fasta(filename)
assert total_reads == 2, total_reads
(total_reads, n_seq_kept) = khmer.filter_fasta_file_limit_n(ht, filename,
total_reads,
outname, 2,
7)
assert total_reads == 2
assert n_seq_kept == 1
(total_reads, n_seq_kept) = khmer.filter_fasta_file_limit_n(ht, filename,
total_reads,
outname, 2,
4)
assert total_reads == 2
assert n_seq_kept == 2
