def _do_trim(self, seq):
'It trims the edges of the given seqs.'
annots = get_annotations(seq)
if not TRIMMING_RECOMMENDATIONS in annots:
return seq
trim_rec = annots[TRIMMING_RECOMMENDATIONS]
# fixing the trimming recommendations
if TRIMMING_RECOMMENDATIONS in annots:
del annots[TRIMMING_RECOMMENDATIONS]
trim_segments = []
for trim_kind in TRIMMING_KINDS:
trim_segments.extend(trim_rec.get(trim_kind, []))
# masking
if self.mask:
seq = _mask_sequence(seq, trim_segments)
else:
# trimming
if trim_segments:
trim_limits = get_longest_complementary_segment(
trim_segments, get_length(seq))
if trim_limits is None:
# there's no sequence left
return None
else:
trim_limits = []
if trim_limits:
seq = slice_seq(seq, trim_limits[0], trim_limits[1] + 1)
return seq
def _do_trim(self, seq):
'It trims the edges of the given seqs.'
annots = get_annotations(seq)
if not TRIMMING_RECOMMENDATIONS in annots:
return seq
trim_rec = annots[TRIMMING_RECOMMENDATIONS]
# fixing the trimming recommendations
if TRIMMING_RECOMMENDATIONS in annots:
del annots[TRIMMING_RECOMMENDATIONS]
trim_segments = []
for trim_kind in TRIMMING_KINDS:
trim_segments.extend(trim_rec.get(trim_kind, []))
# masking
if self.mask:
seq = _mask_sequence(seq, trim_segments)
else:
# trimming
if trim_segments:
trim_limits = get_longest_complementary_segment(
trim_segments, get_length(seq))
if trim_limits is None:
# there's no sequence left
return None
else:
trim_limits = []
if trim_limits:
seq = slice_seq(seq, trim_limits[0], trim_limits[1] + 1)
return seq
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_trimming(self):
'The sequences are trimmed according to the recommendations.'
seq1 = 'gggtctcatcatcaggg'.upper()
seq = SeqRecord(Seq(seq1), annotations={TRIMMING_RECOMMENDATIONS: {}})
seq = SeqWrapper(SEQRECORD, seq, None)
trim_rec = get_annotations(seq)[TRIMMING_RECOMMENDATIONS]
seq_trimmer = TrimOrMask()
trim_rec['vector'] = [(0, 3), (8, 13)]
get_annotations(seq)[TRIMMING_RECOMMENDATIONS] = trim_rec
seqs2 = seq_trimmer([seq])
assert get_str_seq(seqs2[0]) == 'CTCA'
trim_rec['vector'] = [(0, 0), (8, 13)]
get_annotations(seq)[TRIMMING_RECOMMENDATIONS] = trim_rec
seqs2 = seq_trimmer([seq])
assert get_str_seq(seqs2[0]) == 'GGTCTCA'
trim_rec['vector'] = [(0, 1), (8, 12)]
trim_rec['quality'] = [(1, 8), (13, 17)]
get_annotations(seq)[TRIMMING_RECOMMENDATIONS] = trim_rec
seqs2 = seq_trimmer([seq])
assert not seqs2
trim_rec['vector'] = [(0, 0), (8, 13)]
trim_rec['quality'] = []
get_annotations(seq)[TRIMMING_RECOMMENDATIONS] = trim_rec
seqs2 = seq_trimmer([seq])
assert get_str_seq(seqs2[0]) == 'GGTCTCA'
assert TRIMMING_RECOMMENDATIONS not in get_annotations(seqs2[0])
def __call__(self, seqs):
'It trims the edges of the given seqs.'
mask = self.mask
processed_seqs = []
for seq in seqs:
annots = get_annotations(seq)
if not TRIMMING_RECOMMENDATIONS in annots:
processed_seqs.append(copy_seq(seq))
continue
trim_rec = annots[TRIMMING_RECOMMENDATIONS]
# fixing the trimming recommendations
if TRIMMING_RECOMMENDATIONS in annots:
del annots[TRIMMING_RECOMMENDATIONS]
trim_segments = []
for trim_kind in TRIMMING_KINDS:
trim_segments.extend(trim_rec.get(trim_kind, []))
# masking
if mask:
seq = _mask_sequence(seq, trim_segments)
else:
# trimming
if trim_segments:
trim_limits = get_longest_complementary_segment(
trim_segments, get_length(seq))
if trim_limits is None:
# there's no sequence left
continue
else:
trim_limits = []
if trim_limits:
seq = slice_seq(seq, trim_limits[0], trim_limits[1] + 1)
processed_seqs.append(seq)
return processed_seqs
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_trimming(self):
'The sequences are trimmed according to the recommendations.'
seq1 = 'gggtctcatcatcaggg'.upper()
seq = SeqRecord(Seq(seq1), annotations={TRIMMING_RECOMMENDATIONS: {}})
seq = SeqWrapper(SEQRECORD, seq, None)
seqs = [seq]
trim_packet = {SEQS_PASSED: [seqs], ORPHAN_SEQS: []}
trim_rec = get_annotations(seq)[TRIMMING_RECOMMENDATIONS]
seq_trimmer = TrimOrMask()
trim_rec['vector'] = [(0, 3), (8, 13)]
get_annotations(seq)[TRIMMING_RECOMMENDATIONS] = trim_rec
trim_packet2 = seq_trimmer(trim_packet)
res = [get_str_seq(s) for l in trim_packet2[SEQS_PASSED] for s in l]
assert res == ['CTCA']
trim_rec['vector'] = [(0, 0), (8, 13)]
get_annotations(seq)[TRIMMING_RECOMMENDATIONS] = trim_rec
trim_packet2 = seq_trimmer(trim_packet)
res = [get_str_seq(s) for l in trim_packet2[SEQS_PASSED] for s in l]
assert res == ['GGTCTCA']
trim_rec['vector'] = [(0, 1), (8, 12)]
trim_rec['quality'] = [(1, 8), (13, 17)]
get_annotations(seq)[TRIMMING_RECOMMENDATIONS] = trim_rec
trim_packet2 = seq_trimmer(trim_packet)
assert not trim_packet2[SEQS_PASSED]
trim_rec['vector'] = [(0, 0), (8, 13)]
trim_rec['quality'] = []
get_annotations(seq)[TRIMMING_RECOMMENDATIONS] = trim_rec
trim_packet2 = seq_trimmer(trim_packet)
res = [get_str_seq(s) for l in trim_packet2[SEQS_PASSED] for s in l]
assert res == ['GGTCTCA']
trim_packet2[SEQS_PASSED][0][0]
assert TRIMMING_RECOMMENDATIONS not in get_annotations(
trim_packet2[SEQS_PASSED][0][0])
def test_trimming(self):
'The sequences are trimmed according to the recommendations.'
seq1 = 'gggtctcatcatcaggg'.upper()
seq = SeqRecord(Seq(seq1), annotations={TRIMMING_RECOMMENDATIONS: {}})
seq = SeqWrapper(SEQRECORD, seq, None)
seqs = [seq]
trim_packet = {SEQS_PASSED: [seqs], ORPHAN_SEQS: []}
trim_rec = get_annotations(seq)[TRIMMING_RECOMMENDATIONS]
seq_trimmer = TrimOrMask()
trim_rec['vector'] = [(0, 3), (8, 13)]
get_annotations(seq)[TRIMMING_RECOMMENDATIONS] = trim_rec
trim_packet2 = seq_trimmer(trim_packet)
res = [get_str_seq(s) for l in trim_packet2[SEQS_PASSED] for s in l]
assert res == ['CTCA']
trim_rec['vector'] = [(0, 0), (8, 13)]
get_annotations(seq)[TRIMMING_RECOMMENDATIONS] = trim_rec
trim_packet2 = seq_trimmer(trim_packet)
res = [get_str_seq(s) for l in trim_packet2[SEQS_PASSED] for s in l]
assert res == ['GGTCTCA']
trim_rec['vector'] = [(0, 1), (8, 12)]
trim_rec['quality'] = [(1, 8), (13, 17)]
get_annotations(seq)[TRIMMING_RECOMMENDATIONS] = trim_rec
trim_packet2 = seq_trimmer(trim_packet)
assert not trim_packet2[SEQS_PASSED]
trim_rec['vector'] = [(0, 0), (8, 13)]
trim_rec['quality'] = []
get_annotations(seq)[TRIMMING_RECOMMENDATIONS] = trim_rec
trim_packet2 = seq_trimmer(trim_packet)
res = [get_str_seq(s) for l in trim_packet2[SEQS_PASSED] for s in l]
assert res == ['GGTCTCA']
trim_packet2[SEQS_PASSED][0][0]
assert TRIMMING_RECOMMENDATIONS not in get_annotations(trim_packet2[SEQS_PASSED][0][0])
