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_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_blast_short_trimming(self):
'It trims oligos using blast-short'
oligo1 = SeqRecord(Seq('AAGCAGTGGTATCAACGCAGAGTACATGGG'))
oligo2 = SeqRecord(Seq('AAGCAGTGGTATCAACGCAGAGTACTTTTT'))
oligo1 = SeqWrapper(SEQRECORD, oligo1, None)
oligo2 = SeqWrapper(SEQRECORD, oligo2, None)
adaptors = [oligo1, oligo2]
blast_trim = TrimWithBlastShort(oligos=adaptors)
fhand = StringIO(FASTQ4)
seq_packets = read_seq_packets([fhand],
prefered_seq_classes=[SEQRECORD])
trim_packets = list(seq_to_trim_packets(seq_packets))
trim_packets2 = blast_trim(trim_packets[0])
# It should trim the first and the second reads.
res = [
get_annotations(s).get(TRIMMING_RECOMMENDATIONS,
{}).get(VECTOR, [])
for l in trim_packets2[SEQS_PASSED] for s in l
]
assert res == [[(0, 29)], [(0, 29)], []]
# With SeqItems
oligo1 = SeqItem('oligo1',
['>oligo1\n', 'AAGCAGTGGTATCAACGCAGAGTACATGGG\n'])
oligo2 = SeqItem('oligo2',
['>oligo2\n', 'AAGCAGTGGTATCAACGCAGAGTACTTTTT\n'])
oligo1 = SeqWrapper(SEQITEM, oligo1, 'fasta')
oligo2 = SeqWrapper(SEQITEM, oligo2, 'fasta')
adaptors = [oligo1, oligo2]
blast_trim = TrimWithBlastShort(oligos=adaptors)
fhand = StringIO(FASTQ4)
seq_packets = list(
read_seq_packets([fhand], prefered_seq_classes=[SEQITEM]))
trim_packets = list(seq_to_trim_packets(seq_packets))
trim_packets2 = blast_trim(trim_packets[0])
# It should trim the first and the second reads.
res = [
get_annotations(s).get(TRIMMING_RECOMMENDATIONS,
{}).get(VECTOR, [])
for l in trim_packets2[SEQS_PASSED] for s in l
]
assert res == [[(0, 29)], [(0, 29)], []]
def test_blast_short_trimming(self):
'It trims oligos using blast-short'
oligo1 = SeqRecord(Seq('AAGCAGTGGTATCAACGCAGAGTACATGGG'))
oligo2 = SeqRecord(Seq('AAGCAGTGGTATCAACGCAGAGTACTTTTT'))
oligo1 = SeqWrapper(SEQRECORD, oligo1, None)
oligo2 = SeqWrapper(SEQRECORD, oligo2, None)
adaptors = [oligo1, oligo2]
blast_trim = TrimWithBlastShort(oligos=adaptors)
fhand = StringIO(FASTQ4)
seq_packets = read_seq_packets([fhand],
prefered_seq_classes=[SEQRECORD])
trim_packets = list(seq_to_trim_packets(seq_packets))
trim_packets2 = blast_trim(trim_packets[0])
# It should trim the first and the second reads.
res = [get_annotations(s).get(TRIMMING_RECOMMENDATIONS, {}).get(VECTOR,
[])
for l in trim_packets2[SEQS_PASSED] for s in l]
assert res == [[(0, 29)], [(0, 29)], []]
# With SeqItems
oligo1 = SeqItem('oligo1', ['>oligo1\n',
'AAGCAGTGGTATCAACGCAGAGTACATGGG\n'])
oligo2 = SeqItem('oligo2', ['>oligo2\n',
'AAGCAGTGGTATCAACGCAGAGTACTTTTT\n'])
oligo1 = SeqWrapper(SEQITEM, oligo1, 'fasta')
oligo2 = SeqWrapper(SEQITEM, oligo2, 'fasta')
adaptors = [oligo1, oligo2]
blast_trim = TrimWithBlastShort(oligos=adaptors)
fhand = StringIO(FASTQ4)
seq_packets = list(read_seq_packets([fhand],
prefered_seq_classes=[SEQITEM]))
trim_packets = list(seq_to_trim_packets(seq_packets))
trim_packets2 = blast_trim(trim_packets[0])
# It should trim the first and the second reads.
res = [get_annotations(s).get(TRIMMING_RECOMMENDATIONS, {}).get(VECTOR,
[])
for l in trim_packets2[SEQS_PASSED] for s in l]
assert res == [[(0, 29)], [(0, 29)], []]
def test_blast_short_trimming(self):
'It trims oligos using blast-short'
adaptors = [SeqRecord(Seq('AAGCAGTGGTATCAACGCAGAGTACATGGG')),
SeqRecord(Seq('AAGCAGTGGTATCAACGCAGAGTACTTTTT'))]
blast_trim = TrimWithBlastShort(oligos=adaptors)
fhand = StringIO(FASTQ4)
seq_packets = list(read_seq_packets([fhand]))
# It should trim the first and the second reads.
res = [seq.annotations.get(TRIMMING_RECOMMENDATIONS, {}).get(VECTOR, [])
for seq in blast_trim(seq_packets[0])]
assert res == [[(0, 29)], [(0, 29)], []]
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')
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 = '>seq1\1\n'
xpect += 'CTAGTCTAGTCGTAGTCATGGCTGTAGTCTAGTCTACGATTCGTATCAGTTGTGTGAC\n'
xpect += '>seq1\2\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\n'
xpect += 'TGTACTATACACACACGTAGGTCGACTATCGTAGCTAGT\n'
xpect += '>seq5_mlc.part2\n'
xpect += 'ACCTAGTCTAGTCGTAGTCATGGCTGTAGTCTAGTCTACGATTCGTATCAGTTGTGTGAC'
xpect += '\n'
assert xpect == result
def test_filter_by_bowtie2():
index_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
fastq_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
fasta_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fasta')
passed = ['no_arabi']
for preffered_classes in [[SEQITEM], [SEQRECORD]]:
for reads_fpath in [fastq_fpath, fasta_fpath]:
seq_packets = read_seq_packets([open(reads_fpath)],
prefered_seq_classes=preffered_classes)
filter_packets = seq_to_filterpackets(seq_packets)
filter_ = FilterBowtie2Match(index_fpath)
filter_packet = list(filter_packets)[0]
filter_packets = filter_(filter_packet)
assert _seqs_to_names(filter_packets[SEQS_PASSED]) == passed
assert _seqs_to_names(filter_packets[SEQS_FILTERED_OUT]) == [
'read1', 'read2', 'read3']
def test_trim_chimeric_region(self):
index_fpath = os.path.join(TEST_DATA_DIR, 'ref_example.fasta')
query1 = '@seq2 f\nGGGATCGCAGACCCATCTCGTCAGCATGTACCCTTGCTACATTGAACTT'
query1 += 'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n'
query1 += '+\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$'
query1 += '$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n'
query2 = '@seq2 r\nCATCATTGCATAAGTAACACTCAACCAACAGTGCTACAGGGTTGTAACG\n'
query2 += '+\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n'
query = query1 + query2
fhand = NamedTemporaryFile()
fhand.write(query)
fhand.flush()
trim_chimeras = TrimMatePairChimeras(index_fpath)
seq_packets = list(read_seq_packets([open(fhand.name)]))
trim_packets = list(seq_to_trim_packets(seq_packets))
trim_packets2 = trim_chimeras(trim_packets[0])
# It should trim the first and the second reads.
res = [get_annotations(s).get(TRIMMING_RECOMMENDATIONS, {}).get(OTHER,
[])
for l in trim_packets2[SEQS_PASSED] for s in l]
assert res == [[(49, 105)], []]
def test_trim_chimeric_region(self):
index_fpath = os.path.join(TEST_DATA_DIR, 'ref_example.fasta')
query1 = '@seq2 f\nGGGATCGCAGACCCATCTCGTCAGCATGTACCCTTGCTACATTGAACTT'
query1 += 'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n'
query1 += '+\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$'
query1 += '$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n'
query2 = '@seq2 r\nCATCATTGCATAAGTAACACTCAACCAACAGTGCTACAGGGTTGTAACG\n'
query2 += '+\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n'
query = query1 + query2
fhand = NamedTemporaryFile()
fhand.write(query)
fhand.flush()
trim_chimeras = TrimMatePairChimeras(index_fpath)
seq_packets = list(read_seq_packets([open(fhand.name)]))
trim_packets = list(seq_to_trim_packets(seq_packets))
trim_packets2 = trim_chimeras(trim_packets[0])
# It should trim the first and the second reads.
res = [
get_annotations(s).get(TRIMMING_RECOMMENDATIONS,
{}).get(OTHER, [])
for l in trim_packets2[SEQS_PASSED] for s in l
]
assert res == [[(49, 105)], []]
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()