def test_giuseppe_reads():
'It splits some real reads'
seq_fpath = os.path.join(TEST_DATA_DIR, '454_reads.fastq')
linker_fpath = os.path.join(TEST_DATA_DIR, 'linkers.fasta')
linkers = list(read_seqs([open(linker_fpath)]))
splitter = MatePairSplitter(linkers=linkers)
new_seqs = []
for packet in read_seq_packets([open(seq_fpath)], 2):
new_seqs.extend(splitter(packet))
seq_names = [get_name(seq) for seq in new_seqs]
assert 'G109AZL01BJHT8\\1' in seq_names
assert 'G109AZL01BJHT8\\2' in seq_names
assert len(new_seqs) == 20
# test with process_seq_packet
seq_fpath = os.path.join(TEST_DATA_DIR, '454_reads.fastq')
linker_fpath = os.path.join(TEST_DATA_DIR, 'linkers.fasta')
linkers = list(read_seqs([open(linker_fpath)]))
splitter = MatePairSplitter(linkers=linkers)
seq_packets = read_seq_packets([open(seq_fpath)], 2)
seq_packets = process_seq_packets(seq_packets, [splitter])[0]
new_seqs = [seq for l in list(seq_packets) for seq in l]
seq_names = [get_name(seq) for seq in new_seqs]
assert 'G109AZL01BJHT8\\1' in seq_names
assert 'G109AZL01BJHT8\\2' in seq_names
assert len(new_seqs) == 20
# reads 2
seq_fpath = os.path.join(TEST_DATA_DIR, '454_reads2.fastq')
linker_fpath = os.path.join(TEST_DATA_DIR, 'linkers.fasta')
linkers = list(read_seqs([open(linker_fpath)]))
splitter = MatePairSplitter(linkers=linkers)
new_seqs = []
for packet in read_seq_packets([open(seq_fpath)], 2):
new_seqs.extend(splitter(packet))
seq_names = [get_name(seq) for seq in new_seqs]
assert 'G109AZL01D8U3X\\1' in seq_names
assert 'G109AZL01D8U3X\\2' in seq_names
assert len(new_seqs) == 20
# test with process_seq_packet
seq_fpath = os.path.join(TEST_DATA_DIR, '454_reads2.fastq')
linker_fpath = os.path.join(TEST_DATA_DIR, 'linkers.fasta')
linkers = list(read_seqs([open(linker_fpath)]))
splitter = MatePairSplitter(linkers=linkers)
seq_packets = read_seq_packets([open(seq_fpath)], 2)
seq_packets = process_seq_packets(seq_packets, [splitter])[0]
new_seqs = [seq for l in list(seq_packets) for seq in l]
seq_names = [get_name(seq) for seq in new_seqs]
assert 'G109AZL01D8U3X\\1' in seq_names
assert 'G109AZL01D8U3X\\2' in seq_names
assert len(new_seqs) == 20
def test_many_reads(self):
'It splits lots of reads to check that blast finds everything'
linker = TITANIUM_LINKER
def create_seq(index):
'It creates a random seq with a linker'
seq1 = ''.join(choice('ACTG') for i in range(100))
seq2 = ''.join(choice('ACTG') for i in range(100))
seq = seq1 + linker + seq2
seq = SeqRecord(id='seq_' + str(index), seq=Seq(seq))
seq = SeqWrapper(SEQRECORD, seq, None)
return seq
# We want to test that blast reports all reads
packet_size = get_setting('PACKET_SIZE')
default_blast_max_target_size = 500
assert packet_size > default_blast_max_target_size
seqs = [create_seq(i) for i in range(1000)]
splitter = MatePairSplitter()
for index, seq in enumerate(splitter(seqs)):
seq_index = index // 2
pair_index = (index % 2) + 1
expected_id = 'seq_' + str(seq_index) + '\\' + str(pair_index)
assert get_name(seq) == expected_id
def test_split_mate(self):
'It tests the function that splits seqs using segments'
# pylint: disable=W0212
seq = 'aaatttccctt'
seq = SeqWrapper(SEQRECORD, SeqRecord(Seq(seq), id='seq'), None)
# fake class to test
splitter = MatePairSplitter([seq])
# segment beginning
seqs = splitter._split_by_mate_linker(seq, ([(0, 3)], False))
assert get_str_seq(seqs[0]) == 'ttccctt'
assert get_name(seqs[0]) == 'seq'
# segment at end
seqs = splitter._split_by_mate_linker(seq, ([(7, 11)], False))
assert get_str_seq(seqs[0]) == 'aaatttc'
assert get_name(seqs[0]) == 'seq'
# segmnent in the middle
seqs = splitter._split_by_mate_linker(seq, ([(4, 7)], True))
assert get_str_seq(seqs[0]) == 'aaat'
assert get_str_seq(seqs[1]) == 'ctt'
assert get_name(seqs[0]) == 'seq_pl.part1'
assert get_name(seqs[1]) == 'seq_pl.part2'
seqs = splitter._split_by_mate_linker(seq, ([(4, 7)], False))
assert get_name(seqs[0]) == r'seq\1'
assert get_name(seqs[1]) == r'seq\2'
seqs = splitter._split_by_mate_linker(seq, ([(4, 6), (8, 9)], False))
assert get_str_seq(seqs[0]) == 'aaat'
assert get_str_seq(seqs[1]) == 'c'
assert get_str_seq(seqs[2]) == 't'
assert get_name(seqs[0]) == 'seq_mlc.part1'
# all sequence is linker
seqs = splitter._split_by_mate_linker(seq, ([(0, 10)], False))
assert not get_str_seq(seqs[0])
# there's no segments
seqs = splitter._split_by_mate_linker(seq, ([], False))
assert get_name(seq) == get_name(seqs[0])
assert get_str_seq(seq) == get_str_seq(seqs[0])
def test_split_mate(self):
'It tests the function that splits seqs using segments'
# pylint: disable=W0212
seq = 'aaatttccctt'
seqrecord = SeqRecord(Seq(seq), id='seq')
#fake class to test
splitter = MatePairSplitter([seqrecord])
# segment beginning
seqs = splitter._split_by_mate_linker(seqrecord, ([(0, 3)], False))
assert str(seqs[0].seq) == 'ttccctt'
assert seqs[0].id == 'seq'
# segment at end
seqs = splitter._split_by_mate_linker(seqrecord, ([(7, 10)], False))
assert str(seqs[0].seq) == 'aaatttc'
assert seqs[0].id == 'seq'
# segmnet in the middle
seqs = splitter._split_by_mate_linker(seqrecord, ([(4, 7)], True))
assert str(seqs[0].seq) == 'aaat'
assert str(seqs[1].seq) == 'ctt'
assert seqs[0].id == 'seq_pl.part1'
assert seqs[1].id == 'seq_pl.part2'
seqs = splitter._split_by_mate_linker(seqrecord, ([(4, 7)], False))
assert seqs[0].id == 'seq\1'
assert seqs[1].id == 'seq\2'
seqs = splitter._split_by_mate_linker(seqrecord, ([(4, 6), (8, 9)],
False))
assert str(seqs[0].seq) == 'aaat'
assert str(seqs[1].seq) == 'c'
assert str(seqs[2].seq) == 't'
assert seqs[0].id == 'seq_mlc.part1'
# all sequence is linker
seqs = splitter._split_by_mate_linker(seqrecord, ([(0, 10)], False))
assert not str(seqs[0].seq)
# there's no segments
seqs = splitter._split_by_mate_linker(seqrecord, ([], False))
assert seqrecord.id == seqs[0].id
assert str(seqrecord.seq) == str(seqs[0].seq)
def test_split_mate(self):
'It tests the function that splits seqs using segments'
# pylint: disable=W0212
seq = 'aaatttccctt'
seq = SeqWrapper(SEQRECORD, SeqRecord(Seq(seq), id='seq'), None)
# fake class to test
splitter = MatePairSplitter([seq])
# segment beginning
seqs = splitter._split_by_mate_linker(seq, ([(0, 3)], False))
assert get_str_seq(seqs[0]) == 'ttccctt'
assert get_name(seqs[0]) == 'seq'
# segment at end
seqs = splitter._split_by_mate_linker(seq, ([(7, 11)], False))
assert get_str_seq(seqs[0]) == 'aaatttc'
assert get_name(seqs[0]) == 'seq'
# segmnent in the middle
seqs = splitter._split_by_mate_linker(seq, ([(4, 7)], True))
assert get_str_seq(seqs[0]) == 'aaat'
assert get_str_seq(seqs[1]) == 'ctt'
assert get_name(seqs[0]) == 'seq_pl.part1'
assert get_name(seqs[1]) == 'seq_pl.part2'
seqs = splitter._split_by_mate_linker(seq, ([(4, 7)], False))
assert get_name(seqs[0]) == r'seq\1'
assert get_name(seqs[1]) == r'seq\2'
seqs = splitter._split_by_mate_linker(seq, ([(4, 6), (8, 9)],
False))
assert get_str_seq(seqs[0]) == 'aaat'
assert get_str_seq(seqs[1]) == 'c'
assert get_str_seq(seqs[2]) == 't'
assert get_name(seqs[0]) == 'seq_mlc.part1'
# all sequence is linker
seqs = splitter._split_by_mate_linker(seq, ([(0, 10)], False))
assert not get_str_seq(seqs[0])
# there's no segments
seqs = splitter._split_by_mate_linker(seq, ([], False))
assert get_name(seq) == get_name(seqs[0])
assert get_str_seq(seq) == get_str_seq(seqs[0])
def test_split_mates(self):
'It tests the detection of oligos in sequence files'
mate_fhand = NamedTemporaryFile(suffix='.fasta')
linker = TITANIUM_LINKER
# a complete linker
seq5 = 'CTAGTCTAGTCGTAGTCATGGCTGTAGTCTAGTCTACGATTCGTATCAGTTGTGTGAC'
seq3 = 'ATCGATCATGTTGTATTGTGTACTATACACACACGTAGGTCGACTATCGTAGCTAGT'
mate_fhand.write('>seq1\n' + seq5 + linker + seq3 + '\n')
# no linker
mate_fhand.write('>seq2\n' + seq5 + '\n')
# a partial linker
mate_fhand.write('>seq3\n' + seq5 + linker[2:25] + seq3 + '\n')
# the linker is 5 prima
mate_fhand.write('>seq4\n' + linker[10:] + seq3 + '\n')
# two linkers
mate_fhand.write('>seq5\n' + linker + seq3 + FLX_LINKER + seq5 + '\n')
# reverse linker
rev_linker = get_setting('TITANIUM_LINKER_REV')
mate_fhand.write('>seq6\n' + seq5 + rev_linker + seq3 + '\n')
mate_fhand.flush()
splitter = MatePairSplitter()
new_seqs = []
for packet in read_seq_packets([mate_fhand], 2):
new_seqs.append(splitter(packet))
out_fhand = StringIO()
write_seq_packets(out_fhand, new_seqs, file_format='fasta')
result = out_fhand.getvalue()
xpect = r'>seq1\1'
xpect += '\n'
xpect += 'CTAGTCTAGTCGTAGTCATGGCTGTAGTCTAGTCTACGATTCGTATCAGTTGTGTGAC\n'
xpect += r'>seq1\2'
xpect += '\n'
xpect += 'ATCGATCATGTTGTATTGTGTACTATACACACACGTAGGTCGACTATCGTAGCTAGT\n'
xpect += '>seq2\n'
xpect += 'CTAGTCTAGTCGTAGTCATGGCTGTAGTCTAGTCTACGATTCGTATCAGTTGTGTGAC\n'
xpect += '>seq3_pl.part1\n'
xpect += 'CTAGTCTAGTCGTAGTCATGGCTGTAGTCTAGTCTACGATTCGTATCAGTTGTGTG\n'
xpect += '>seq3_pl.part2\n'
xpect += 'GTGTACTATACACACACGTAGGTCGACTATCGTAGCTAGT\n'
xpect += '>seq4\n'
xpect += 'ATCGATCATGTTGTATTGTGTACTATACACACACGTAGGTCGACTATCGTAGCTAGT\n'
xpect += '>seq5_mlc.part1\n'
xpect += 'TCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGATCGATCATGTTGTAT'
xpect += 'TG'
xpect += 'TGTACTATACACACACGTAGGTCGACTATCGTAGCTAGT\n'
xpect += '>seq5_mlc.part2\n'
xpect += 'ACCTAGTCTAGTCGTAGTCATGGCTGTAGTCTAGTCTACGATTCGTATCAGTTGTGTGAC'
xpect += '\n'
xpect += r'>seq6\1'
xpect += '\n'
xpect += 'CTAGTCTAGTCGTAGTCATGGCTGTAGTCTAGTCTACGATTCGTATCAGTTGTGTGAC\n'
xpect += r'>seq6\2'
xpect += '\n'
xpect += 'ATCGATCATGTTGTATTGTGTACTATACACACACGTAGGTCGACTATCGTAGCTAGT\n'
assert xpect == result
# with short linker in 3 prima
mate_fhand = NamedTemporaryFile(suffix='.fasta')
seq = ">seq1\nCATCAATGACATCACAAATGACATCAACAAACTCAAA"
seq += "CTCACATACACTGCTGTACCGTAC"
mate_fhand.write(seq)
mate_fhand.flush()
splitter = MatePairSplitter()
new_seqs = []
for packet in read_seq_packets([mate_fhand], 1):
new_seqs.append(splitter(packet))
out_fhand = StringIO()
write_seq_packets(out_fhand, new_seqs, file_format='fasta')
result = ">seq1\nCATCAATGACATCACAAATGACATCAACAAACTCAAACTCACATACA\n"
assert result == out_fhand.getvalue()