def test_take_sample():
'tests take sample test'
#basic test
items = iter(range(100))
sample = list(take_sample(items, 10))
assert len(sample) == 10
assert sample != [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
n_items = [1000, 100, 100000, 100000, 100000]
sample_sizes = [990, 8, 100, 100, 200]
for n_item, sample_size in zip(n_items, sample_sizes):
repeats = 0
while repeats < 10:
repeats += 1
iterator= iter(range(n_item))
a = take_sample(iterator, sample_size)
assert sample_size == len(list(a))
def seqs_in_file(seq_fhand, qual_fhand=None, format=None, sample_size=None,
double_encoding=False):
'It yields a seqrecord for each of the sequences found in the seq file.'
if format is None:
format = guess_seq_file_format(seq_fhand)
seqs =_seqs_in_file(seq_fhand, qual_fhand=qual_fhand, file_format=format,
double_encoding=double_encoding)
if sample_size is None:
return seqs
try:
num_seqs = num_seqs_in_file(seq_fhand, format)
except NotImplementedError:
num_seqs = None
return take_sample(seqs, sample_size, num_seqs)
def sample_bam(bam_fhand, out_bam_fhand, sample_size):
'It takes a sample from a bam'
sam_fhand = NamedTemporaryFile(suffix='.sam')
final_sam = NamedTemporaryFile(suffix='.sam')
bam2sam(bam_fhand.name, sam_fhand.name, header=True)
# First get header
for line in open(sam_fhand.name):
if line[0] == '@':
final_sam.write(line)
else:
break
sam_body = take_sample(_reads_in_sam(sam_fhand), sample_size=sample_size)
for line in sam_body:
final_sam.write(line)
final_sam.flush()
sam2bam(final_sam.name, out_bam_fhand.name)
def test_tee_sample(self):
'It tests that tee and sample behave ok together'
items = iter(range(1000))
sample = take_sample(items, 50)
sample1, sample2 = itertools.tee(sample)
