def _test_filter_duplicates(paired_reads, n_seqs_packet):
assert isinstance(n_seqs_packet, int) or n_seqs_packet == None
in_fhand = NamedTemporaryFile()
fastq_with_dups = (FASTQ_NO_DUPS1 + FASTQ_DUPS + FASTQ_NO_DUPS2
+ FASTQ_NO_DUPS3)
in_fhand.write(fastq_with_dups)
in_fhand.flush()
in_fhand = open(in_fhand.name)
out_fhand = NamedTemporaryFile()
filter_duplicates([in_fhand], out_fhand, paired_reads, n_seqs_packet)
flush_fhand(out_fhand)
filtered_pairs = list(_read_pairs([open(out_fhand.name)],
paired_reads))
fastq_no_dups = FASTQ_NO_DUPS1 + FASTQ_NO_DUPS2 + FASTQ_NO_DUPS3
expected_pairs = list(_read_pairs([StringIO(fastq_no_dups)],
paired_reads))
#print 'filtered_pairs ->', filtered_pairs
#print 'expected_pairs ->', expected_pairs
#print len(filtered_pairs), len(expected_pairs)
#assert len(filtered_pairs) == len(expected_pairs)
for pair1 in expected_pairs:
counts = 0
for pair2 in filtered_pairs:
if _seqitem_pairs_equal(pair1, pair2):
counts += 1
assert counts == 1
in_fhand.close()
def _test_filter_duplicates(paired_reads, n_seqs_packet):
assert isinstance(n_seqs_packet, int) or n_seqs_packet == None
in_fhand = NamedTemporaryFile()
fastq_with_dups = (FASTQ_NO_DUPS1 + FASTQ_DUPS + FASTQ_NO_DUPS2 +
FASTQ_NO_DUPS3)
in_fhand.write(fastq_with_dups)
in_fhand.flush()
in_fhand = open(in_fhand.name)
out_fhand = NamedTemporaryFile()
filter_duplicates([in_fhand], out_fhand, paired_reads, n_seqs_packet)
flush_fhand(out_fhand)
filtered_pairs = list(_read_pairs([open(out_fhand.name)], paired_reads))
fastq_no_dups = FASTQ_NO_DUPS1 + FASTQ_NO_DUPS2 + FASTQ_NO_DUPS3
expected_pairs = list(_read_pairs([StringIO(fastq_no_dups)], paired_reads))
#print 'filtered_pairs ->', filtered_pairs
#print 'expected_pairs ->', expected_pairs
#print len(filtered_pairs), len(expected_pairs)
#assert len(filtered_pairs) == len(expected_pairs)
for pair1 in expected_pairs:
counts = 0
for pair2 in filtered_pairs:
if _seqitem_pairs_equal(pair1, pair2):
counts += 1
assert counts == 1
in_fhand.close()
# use length
in_fhand = NamedTemporaryFile()
in_fhand.write(FASTQ_DUPS)
in_fhand.flush()
in_fhand = open(in_fhand.name)
out_fhand = NamedTemporaryFile()
filter_duplicates([in_fhand],
out_fhand,
paired_reads=False,
n_seqs_packet=n_seqs_packet,
use_length=10)
flush_fhand(out_fhand)
filtered_pairs = list(
_read_pairs([open(out_fhand.name)], paired_reads=False))
assert len(filtered_pairs) == 2
# use length
in_fhand = NamedTemporaryFile()
in_fhand.write(FASTQ_DUPS)
in_fhand.flush()
in_fhand = open(in_fhand.name)
out_fhand = NamedTemporaryFile()
filter_duplicates([in_fhand],
out_fhand,
paired_reads=False,
n_seqs_packet=n_seqs_packet,
use_length=1)
flush_fhand(out_fhand)
filtered_pairs = list(
_read_pairs([open(out_fhand.name)], paired_reads=False))
assert len(filtered_pairs) == 1
def test_seqitem_pairs_equal(self):
seq1 = SeqWrapper(SEQITEM, SeqItem('seq1',
['@seq1\n', 'TAATAC\n', '+\n',
'TTTDFG\n']), 'fastq')
seq2 = SeqWrapper(SEQITEM, SeqItem('seq2',
['@seq2\n', 'TCATTA\n', '+\n',
'ABCBEG\n']), 'fastq')
seq3 = SeqWrapper(SEQITEM, SeqItem('seq3',
['@seq3\n', 'TAATAC\n', '+\n',
'TTTDFG\n']), 'fastq')
seq4 = SeqWrapper(SEQITEM, SeqItem('seq4',
['@seq4\n', 'ACGCGT\n', '+\n',
'ABCBEG\n']), 'fastq')
pair1 = (seq1, seq2)
pair2 = (seq2, seq4)
pair3 = (seq3, seq2)
pair4 = (seq2, seq1)
assert _seqitem_pairs_equal(pair1, pair3)
assert not _seqitem_pairs_equal(pair1, pair2)
assert not _seqitem_pairs_equal(pair1, pair4)
assert _seqitem_pairs_equal([seq1], [seq3])
assert not _seqitem_pairs_equal([seq1], [seq2])
assert not _seqitem_pairs_equal([seq1], pair1)
assert not _seqitem_pairs_equal(pair1, seq2)
def test_seqitem_pairs_equal(self):
seq1 = SeqWrapper(
SEQITEM, SeqItem('seq1',
['@seq1\n', 'TAATAC\n', '+\n', 'TTTDFG\n']),
'fastq')
seq2 = SeqWrapper(
SEQITEM, SeqItem('seq2',
['@seq2\n', 'TCATTA\n', '+\n', 'ABCBEG\n']),
'fastq')
seq3 = SeqWrapper(
SEQITEM, SeqItem('seq3',
['@seq3\n', 'TAATAC\n', '+\n', 'TTTDFG\n']),
'fastq')
seq4 = SeqWrapper(
SEQITEM, SeqItem('seq4',
['@seq4\n', 'ACGCGT\n', '+\n', 'ABCBEG\n']),
'fastq')
pair1 = (seq1, seq2)
pair2 = (seq2, seq4)
pair3 = (seq3, seq2)
pair4 = (seq2, seq1)
assert _seqitem_pairs_equal(pair1, pair3)
assert not _seqitem_pairs_equal(pair1, pair2)
assert not _seqitem_pairs_equal(pair1, pair4)
assert _seqitem_pairs_equal([seq1], [seq3])
assert not _seqitem_pairs_equal([seq1], [seq2])
assert not _seqitem_pairs_equal([seq1], pair1)
assert not _seqitem_pairs_equal(pair1, seq2)
def test_seqitem_pairs_equal(self):
seq1 = SeqWrapper(SEQITEM, SeqItem("seq1", ["@seq1\n", "TAATAC\n", "+\n", "TTTDFG\n"]), "fastq")
seq2 = SeqWrapper(SEQITEM, SeqItem("seq2", ["@seq2\n", "TCATTA\n", "+\n", "ABCBEG\n"]), "fastq")
seq3 = SeqWrapper(SEQITEM, SeqItem("seq3", ["@seq3\n", "TAATAC\n", "+\n", "TTTDFG\n"]), "fastq")
seq4 = SeqWrapper(SEQITEM, SeqItem("seq4", ["@seq4\n", "ACGCGT\n", "+\n", "ABCBEG\n"]), "fastq")
pair1 = (seq1, seq2)
pair2 = (seq2, seq4)
pair3 = (seq3, seq2)
pair4 = (seq2, seq1)
assert _seqitem_pairs_equal(pair1, pair3)
assert _seqitem_pairs_equal(pair1, pair2) == False
assert _seqitem_pairs_equal(pair1, pair4) == False
assert _seqitem_pairs_equal([seq1], [seq3])
assert _seqitem_pairs_equal([seq1], [seq2]) == False
assert _seqitem_pairs_equal([seq1], pair1) == False
assert _seqitem_pairs_equal(pair1, seq2) == False
