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_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)], []]
