def test_slice(self):
# with fasta
seq = SeqItem(name='s1', lines=['>s1\n', 'ACTG\n', 'GTAC\n'])
seq = SeqWrapper(SEQITEM, seq, 'fasta')
expected_seq = SeqItem(name='s1', lines=['>s1\n', 'CTGG\n'])
expected_seq = SeqWrapper(SEQITEM, expected_seq, 'fasta')
assert slice_seq(seq, 1, 5) == expected_seq
# with fastq
seq = SeqItem(name='seq', lines=['@seq\n', 'aata\n', '+\n', '!?!?\n'])
seq = SeqWrapper(SEQITEM, seq, 'fastq')
seq = slice_seq(seq, 1, 3)
assert list(get_qualities(seq)) == [30, 0]
assert get_str_seq(seq) == 'at'
assert seq.object.lines == ['@seq\n', 'at\n', '+\n', '?!\n']
# with multiline fastq
seq = SeqItem(
name='seq',
lines=['@seq\n', 'aaat\n', 'caaa\n', '+\n', '@AAA\n', 'BBBB\n'])
seq = SeqWrapper(SEQITEM, seq, 'fastq-illumina-multiline')
seq_ = slice_seq(seq, 1, 5)
assert list(get_qualities(seq_)) == [1, 1, 1, 2]
assert get_str_seq(seq_) == get_str_seq(seq)[1:5]
# It tests the stop is None
seq = SeqItem('seq', ['>seq\n', 'aCTG'])
seq = SeqWrapper(SEQITEM, seq, 'fasta')
assert get_str_seq(slice_seq(seq, 1, None)) == 'aCTG'[1:]
assert get_str_seq(slice_seq(seq, None, 1)) == 'aCTG'[:1]
def test_str_qualities(self):
# with fasta
seq = SeqItem(name='s1', lines=['>s1\n', 'ACTG\n', 'GTAC\n'])
seq = SeqWrapper(SEQITEM, seq, 'fasta')
try:
assert get_str_qualities(seq, 'fasta')
self.fail('ValueError expected')
except ValueError:
pass
# with fastq
seq = SeqItem(name='seq', lines=['@seq\n', 'aaaa\n', '+\n', '!???\n'])
seq = SeqWrapper(SEQITEM, seq, 'fastq')
assert get_str_qualities(seq) == '!???'
# with fastq to fastq-illumina
seq = SeqItem(name='seq', lines=['@seq\n', 'aaaa\n', '+\n', '!???\n'])
seq = SeqWrapper(SEQITEM, seq, 'fastq')
assert get_str_qualities(seq, ILLUMINA_QUALITY) == '@^^^'
# with multiline fastq-illumina
seq = SeqItem(name='seq',
lines=['@seq\n', 'aaaaaaaa\n', '+\n', '@AAABBBB\n'])
seq = SeqWrapper(SEQITEM, seq, 'fastq-illumina')
assert get_str_qualities(seq, ILLUMINA_QUALITY) == '@AAABBBB'
# with multiline fastq-illumina to fastq
seq = SeqItem(name='seq',
lines=['@seq\n', 'aaaaaaaa\n', '+\n', '@AAABBBB\n'])
seq = SeqWrapper(SEQITEM, seq, 'fastq-illumina')
assert get_str_qualities(seq, 'fastq') == '!"""####'
def _build_some_paired_seqs():
seq1 = SeqWrapper(SEQITEM, SeqItem('s1', ['>s1.f\n', 'A\n']), 'fasta')
seq2 = SeqWrapper(SEQITEM, SeqItem('s1', ['>s1.r\n', 'C\n']), 'fasta')
seq3 = SeqWrapper(SEQITEM, SeqItem('s2', ['>s2.f\n', 'T\n']), 'fasta')
seq4 = SeqWrapper(SEQITEM, SeqItem('s2', ['>s2.r\n', 'G\n']), 'fasta')
seqs = seq1, seq2, seq3, seq4
return seqs
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 _itemize_fastx_multiline(fhand): # this is a generator function
last_line = None # this is a buffer keeping the last unprocessed line
is_empty = True
n_single_line_seqs = 0
n_seqs_read = 0
while True: # mimic closure; is it a bad idea?
if not last_line: # the first record or a record following a fastq
for line in fhand: # search for the start of the next record
if line[0] in '@>': # fasta/q header line
last_line = line # save this line
break
if not last_line:
break
title = last_line
seq_lines = []
last_line = None
name = title[1:-1].partition(" ")[0]
for line in fhand: # read the sequence
if line[0] in '@+>':
last_line = line
break
seq_lines.append(line.rstrip())
if not last_line or last_line[0] != '+': # this is a fasta record
yield SeqItem(name, [title, ''.join(seq_lines) + '\n'])
n_seqs_read += 1
is_empty = False
if not last_line:
break
else: # this is a fastq record
seq = ''.join(seq_lines)
length = 0
qual_lines = []
len_seq = len(seq)
for line in fhand: # read the quality
qual_lines.append(line.rstrip())
length += len(line) - 1
if length >= len_seq: # have read enough quality
if length != len_seq:
msg = 'Malformed fastq file: seq and quality lines'
msg += 'have different lengths'
raise MalformedFile(msg)
last_line = None
is_empty = False
yield SeqItem(name, [title, seq + '\n', '+\n',
''.join(qual_lines) + '\n'])
n_seqs_read += 1
if len(qual_lines) == 1:
n_single_line_seqs += 1
if n_seqs_read == 1000:
if n_single_line_seqs == n_seqs_read:
raise IsSingleLineFastqError()
break
if last_line: # reach EOF before reading enough quality
msg = 'Malformed fastq file: quality line missing'
raise MalformedFile(msg)
if is_empty:
raise FileIsEmptyError('File is empty')
def test_trim_seqs():
'It tests the trim seq function'
seqs = []
seqs.append([SeqWrapper(SEQRECORD, SeqRecord(Seq('aaCTTTC')), None)])
seqs.append([SeqWrapper(SEQRECORD, SeqRecord(Seq('CTTCaa')), None)])
seqs.append([SeqWrapper(SEQRECORD, SeqRecord(Seq('aaCTCaa')), None)])
seqs.append([SeqWrapper(SEQRECORD, SeqRecord(Seq('actg')), None)])
seqs.append([SeqWrapper(SEQRECORD, SeqRecord(Seq('AC')), None)])
trim_packet = {SEQS_PASSED: seqs, ORPHAN_SEQS: []}
trim_lowercased_seqs = TrimLowercasedLetters()
trim = TrimOrMask()
# pylint: disable=W0141
trim_packet = trim(trim_lowercased_seqs(trim_packet))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
assert res == ['CTTTC', 'CTTC', 'CTC', 'AC']
seqs = []
seq = SeqItem('s', ['>s\n', 'aaCTTTC\n'])
seqs.append([SeqWrapper(SEQITEM, seq, 'fasta')])
trim_packet = {SEQS_PASSED: seqs, ORPHAN_SEQS: []}
trim_packet = trim(trim_lowercased_seqs(trim_packet))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
assert res == ['CTTTC']
# with pairs
seq = SeqItem('s.f', ['>s.f\n', 'aaCTTTC\n'])
seq1 = SeqItem('s.r', ['>s.r\n', 'aaCTTTC\n'])
seq2 = SeqItem('s1.f', ['>s1.f\n', 'aa\n'])
seq3 = SeqItem('s1.r', ['>s1.r\n', 'aaCTTTC\n'])
seqs = []
seqs.append([SeqWrapper(SEQITEM, seq, 'fasta'),
SeqWrapper(SEQITEM, seq1, 'fasta')])
seqs.append([SeqWrapper(SEQITEM, seq2, 'fasta'),
SeqWrapper(SEQITEM, seq3, 'fasta')])
trim_packet = {SEQS_PASSED: seqs, ORPHAN_SEQS: []}
trim_lowercased_seqs = TrimLowercasedLetters()
trim = TrimOrMask()
# pylint: disable=W0141
trim_packet = trim(trim_lowercased_seqs(trim_packet))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
orphan_res = [get_str_seq(s) for s in trim_packet[ORPHAN_SEQS]]
assert orphan_res == ['CTTTC']
assert ['CTTTC', 'CTTTC'] == res
# no drag
trim_packet = {SEQS_PASSED: seqs, ORPHAN_SEQS: []}
trim_lowercased_seqs = TrimLowercasedLetters()
trim = TrimOrMask()
# pylint: disable=W0141
trim_packet = trim(trim_lowercased_seqs(trim_packet))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
orphan_res = [get_name(s) for s in trim_packet[ORPHAN_SEQS]]
assert orphan_res == ['s1.r']
assert ['CTTTC', 'CTTTC'] == res
def test_str_seq(self):
# with fasta
seq = SeqItem(name='s1', lines=['>s1\n', 'ACTGGTAC\n'])
seq = SeqWrapper(SEQITEM, seq, 'fasta')
assert get_str_seq(seq) == 'ACTGGTAC'
# with fastq
seq = SeqItem(name='seq', lines=['@seq\n', 'aaaa\n', '+\n', '????\n'])
seq = SeqWrapper(SEQITEM, seq, 'fastq')
assert get_str_seq(seq) == 'aaaa'
def test_pair_grouper():
seq1 = SeqWrapper(SEQITEM, SeqItem('s1', ['>s1.f\n', 'A\n']), 'fasta')
seq2 = SeqWrapper(SEQITEM, SeqItem('s1', ['>s1.r\n', 'C\n']), 'fasta')
seq3 = SeqWrapper(SEQITEM, SeqItem('s2', ['>s2.f\n', 'T\n']), 'fasta')
seq4 = SeqWrapper(SEQITEM, SeqItem('s2', ['>s2.r\n', 'G\n']), 'fasta')
seqs = seq1, seq2, seq3, seq4
paired_seqs = list(group_seqs_in_pairs(seqs))
assert [get_str_seq(s) for s in paired_seqs[0]] == ['A', 'C']
assert [get_str_seq(s) for s in paired_seqs[1]] == ['T', 'G']
assert len(paired_seqs) == 2
def test_len(self):
# with fasta
seq = SeqItem(name='s1', lines=['>s1\n', 'ACTG\n', 'GTAC\n'])
seq = SeqWrapper(SEQITEM, seq, 'fasta')
assert get_length(seq) == 8
# with fastq
seq = SeqItem(name='seq', lines=['@seq\n', 'aaaa\n', '+\n', '????\n'])
seq = SeqWrapper(SEQITEM, seq, 'fastq')
assert get_length(seq) == 4
def test_change_name(self):
seq = SeqItem(name='seq',
lines=['@seq\n', 'aaaa\n', '+seq\n', '!???\n'])
seq = SeqWrapper(SEQITEM, seq, 'fastq')
seq = copy_seq(seq, name='seq2')
assert seq.object == ('seq2', ['@seq2\n', 'aaaa\n', '+\n',
'!???\n'], {})
seq = SeqItem(name='seq', lines=['>seq\n', 'aaaa\n'])
seq = SeqWrapper(SEQITEM, seq, 'fasta')
seq = copy_seq(seq, name='seq2')
assert seq.object == ('seq2', ['>seq2\n', 'aaaa\n'], {})
def __init__(self, linkers=None):
'The initiator'
if linkers is None:
linkers = get_setting('LINKERS')
linkers = [SeqItem(str(i), '>%d\n%s\n' % (i, l)) for i, l in enumerate(linkers)]
linkers = assing_kind_to_seqs(SEQITEM, linkers, 'fasta')
self.linkers = list(linkers)
def test_no_name(self):
seqs = _build_some_paired_seqs()
seq = SeqWrapper(SEQITEM, SeqItem('s', ['>s\n', 'N\n']), 'fasta')
seqs = seqs[0], seqs[1], seqs[2], seq, seqs[3]
paired_seqs = list(group_pairs_by_name(seqs))
assert [get_str_seq(s) for s in paired_seqs[0]] == ['A', 'C']
assert [get_str_seq(s) for s in paired_seqs[1]] == ['T']
assert [get_str_seq(s) for s in paired_seqs[2]] == ['N']
assert [get_str_seq(s) for s in paired_seqs[3]] == ['G']
seqs = _build_some_paired_seqs()
seqs = seqs[0], seq, seqs[1], seqs[2], seqs[3]
paired_seqs = list(group_pairs_by_name(seqs))
assert [get_str_seq(s) for s in paired_seqs[0]] == ['A']
assert [get_str_seq(s) for s in paired_seqs[1]] == ['N']
assert [get_str_seq(s) for s in paired_seqs[2]] == ['C']
assert [get_str_seq(s) for s in paired_seqs[3]] == ['T', 'G']
seqs = _build_some_paired_seqs()
seqs = seq, seqs[0], seqs[1], seqs[2], seqs[3]
paired_seqs = list(group_pairs_by_name(seqs))
assert [get_str_seq(s) for s in paired_seqs[0]] == ['N']
assert [get_str_seq(s) for s in paired_seqs[1]] == ['A', 'C']
assert [get_str_seq(s) for s in paired_seqs[2]] == ['T', 'G']
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 _itemize_fasta(fhand):
'It returns the fhand divided in chunks, one per seq'
lines = []
for line in fhand:
if not line or line.isspace():
continue
if line.startswith('>'):
if lines:
yield SeqItem(_get_name_from_lines(lines), lines)
lines = []
lines.append(line)
if len(lines) == 1 and not lines[0].startswith('>'):
raise RuntimeError('Not a valid fasta file')
else:
if lines:
yield SeqItem(_get_name_from_lines(lines), lines)
def test_matching_segments(self):
'It tests the detection of oligos in sequence files'
seq_5 = 'CTAGTCTAGTCGTAGTCATGGCTGTAGTCTAGTCTACGATTCGTATCAGTTGTGTGAC'
mate_fhand = create_a_matepair_file()
linkers = [
SeqItem('titan', ['>titan\n', TITANIUM_LINKER + '\n']),
SeqItem('flx', ['>flx\n', FLX_LINKER + '\n'])
]
linkers = assing_kind_to_seqs(SEQITEM, linkers, 'fasta')
expected_region = (len(seq_5), len(seq_5 + TITANIUM_LINKER) - 1)
matcher = BlasterForFewSubjects(mate_fhand.name,
linkers,
program='blastn',
elongate_for_global=True)
linker_region = matcher.get_matched_segments_for_read('seq1')[0]
assert [expected_region] == linker_region
def test_int_qualities(self):
# with fasta
seq = SeqItem(name='s1', lines=['>s1\n', 'ACTG\n', 'GTAC\n'])
seq = SeqWrapper(SEQITEM, seq, 'fasta')
try:
assert get_int_qualities(seq)
self.fail('AttributeError expected')
except AttributeError:
pass
# with fastq
seq = SeqItem(name='seq', lines=['@seq\n', 'aaaa\n', '+\n', '!???\n'])
seq = SeqWrapper(SEQITEM, seq, 'fastq')
assert list(get_int_qualities(seq)) == [0, 30, 30, 30]
seq = SeqItem(name='seq',
lines=['@seq\n', 'aaaaaaaa\n', '+\n', '@AAABBBB\n'])
seq = SeqWrapper(SEQITEM, seq, 'fastq-illumina')
assert list(get_int_qualities(seq)) == [0, 1, 1, 1, 2, 2, 2, 2]
def test_copy(self):
# with fasta
seq = SeqItem(name='s1',
lines=['>s1\n', 'ACTG\n', 'GTAC\n'],
annotations={'a': 'b'})
seq = SeqWrapper(SEQITEM, seq, 'fasta')
seq2 = copy_seq(seq, seq='ACTG')
assert seq2.object == SeqItem(name='s1',
lines=['>s1\n', 'ACTG\n'],
annotations={'a': 'b'})
assert seq.object is not seq2.object
assert seq.object.lines is not seq2.object.lines
# with fastq
seq = SeqItem(name='seq', lines=['@seq\n', 'aaaa\n', '+\n', '!???\n'])
seq = SeqWrapper(SEQITEM, seq, 'fastq')
seq2 = copy_seq(seq, seq='ACTG')
assert seq2.object == SeqItem(
name='seq', lines=['@seq\n', 'ACTG\n', '+\n', '!???\n'])
# with multiline fastq
seq = SeqItem(
name='seq',
lines=['@seq\n', 'aaaa\n', 'aaaa\n', '+\n', '@AAA\n', 'BBBB\n'])
seq = SeqWrapper(SEQITEM, seq, 'fastq-illumina-multiline')
seq2 = copy_seq(seq, seq='ACTGactg')
assert seq2.object == SeqItem(
name='seq', lines=['@seq\n', 'ACTGactg\n', '+\n', '@AAABBBB\n'])
def alignedread_to_seqitem(aligned_read, start_pos=0, end_pos=None):
if aligned_read is None or aligned_read.seq is None:
return None
name = aligned_read.qname
seq = aligned_read.seq[start_pos: end_pos]
quals = aligned_read.qual
if aligned_read.is_reverse:
seq = _reverse(_complementary(seq))
if quals is None:
lines = ['>' + name + '\n', seq + '\n']
file_format = 'fasta'
else:
quals = quals[start_pos: end_pos]
if aligned_read.is_reverse:
quals = _reverse(quals)
lines = ['@' + name + '\n', seq + '\n', '+\n', quals + '\n']
file_format = 'fastq'
return SeqWrapper(SEQITEM, SeqItem(name, lines), file_format)
def test_edge_trimming(self):
'It trims the edges'
trim = TrimOrMask()
trim_edges = TrimEdges(left=1)
trim_packet = trim(trim_edges(self._some_seqs()))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
assert res == ['CCG', 'AACCCGGG']
trim_edges = TrimEdges(right=1)
trim_packet = trim(trim_edges(self._some_seqs()))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
assert res == ['ACC', 'AAACCCGG']
trim_edges = TrimEdges(left=1, right=1)
trim_packet = trim(trim_edges(self._some_seqs()))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
assert res == ['CC', 'AACCCGG']
trim_edges = TrimEdges(left=2, right=2)
trim_packet = trim(trim_edges(self._some_seqs()))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
assert res == ['ACCCG']
trim_edges = TrimEdges(left=3, right=3)
trim_packet = trim(trim_edges(self._some_seqs()))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
assert res == ['CCC']
trim = TrimOrMask(mask=True)
trim_edges = TrimEdges(left=1)
trim_packet = trim(trim_edges(self._some_seqs()))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
assert res == ['aCCG', 'aAACCCGGG']
trim_edges = TrimEdges(right=1)
trim_packet = trim(trim_edges(self._some_seqs()))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
assert res == ['ACCg', 'AAACCCGGg']
trim_edges = TrimEdges(left=1, right=1)
trim_packet = trim(trim_edges(self._some_seqs()))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
assert res == ['aCCg', 'aAACCCGGg']
trim_edges = TrimEdges(left=2, right=2)
trim_packet = trim(trim_edges(self._some_seqs()))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
assert res == ['accg', 'aaACCCGgg']
trim_edges = TrimEdges(left=3, right=3)
trim_packet = trim(trim_edges(self._some_seqs()))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
assert res == ['accg', 'aaaCCCggg']
# test overlapping mask
trim1 = TrimEdges(left=3, right=3)
trim2 = TrimEdges(left=4, right=4)
trim_packet = trim(trim2(trim1(self._some_seqs())))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
assert res == ['accg', 'aaacCcggg']
# With a SeqItem
trim = TrimOrMask(mask=False)
trim_edges = TrimEdges(left=1, right=1)
seq = SeqItem('s', ['>s\n', 'ACTTTC\n'])
seqs = [[SeqWrapper(SEQITEM, seq, 'fasta')]]
trim_packet = {SEQS_PASSED: seqs, ORPHAN_SEQS: []}
trim_packet = trim(trim_edges(trim_packet))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
assert res == ['CTTT']
trim = TrimOrMask(mask=True)
seq = SeqItem('s', ['>s\n', 'ACTTTC\n'])
seqs = [[SeqWrapper(SEQITEM, seq, 'fasta')]]
trim_packet = {SEQS_PASSED: seqs, ORPHAN_SEQS: []}
trim_packet = trim(trim_edges(trim_packet))
res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
assert res == ['aCTTTc']
def test_quality_trimming(self):
'It trims the edges'
trim = TrimOrMask()
trim_quality = TrimByQuality(window=5, threshold=30)
seq = SeqRecord(Seq('ACTGCTGCATAAAA'))
quals = [10, 10, 20, 30, 30, 30, 40, 40, 30, 30, 20, 20, 10, 10]
seq.letter_annotations['phred_quality'] = quals
seq = SeqWrapper(SEQRECORD, seq, None)
trim_packet = {SEQS_PASSED: [[seq]], ORPHAN_SEQS: []}
trim_packet2 = trim(trim_quality(trim_packet))
seq2 = trim_packet2[SEQS_PASSED][0][0]
assert get_int_qualities(seq2) == [20, 30, 30, 30, 40, 40, 30, 30, 20]
# all bad
trim_quality = TrimByQuality(window=5, threshold=60)
trim_packet = {SEQS_PASSED: [[seq]], ORPHAN_SEQS: []}
trim_packet2 = trim(trim_quality(trim_packet))
assert not trim_packet2[SEQS_PASSED]
# all OK
trim_quality = TrimByQuality(window=5, threshold=5)
trim_packet = {SEQS_PASSED: [[seq]], ORPHAN_SEQS: []}
trim_packet2 = trim(trim_quality(trim_packet))
seq2 = trim_packet2[SEQS_PASSED][0][0]
assert get_int_qualities(seq2) == quals
seq = SeqRecord(Seq('ACTGCTGCATAA'))
quals = [20, 20, 20, 60, 60, 60, 60, 60, 20, 20, 20, 20]
trim_quality = TrimByQuality(window=5, threshold=50)
seq.letter_annotations['phred_quality'] = quals
seq = SeqWrapper(SEQRECORD, seq, None)
trim_packet = {SEQS_PASSED: [[seq]], ORPHAN_SEQS: []}
trim_packet2 = trim(trim_quality(trim_packet))
seq2 = trim_packet2[SEQS_PASSED][0][0]
assert get_int_qualities(seq2) == [20, 60, 60, 60, 60, 60, 20]
quals = [
40, 18, 10, 40, 40, 5, 8, 30, 14, 3, 40, 40, 40, 11, 6, 5, 3, 20,
10, 12, 8, 5, 4, 7, 1
]
seq = SeqRecord(Seq('atatatatagatagatagatagatg'))
seq.letter_annotations['phred_quality'] = quals
seq = SeqWrapper(SEQRECORD, seq, None)
trim_packet = {SEQS_PASSED: [[seq]], ORPHAN_SEQS: []}
trim_quality = TrimByQuality(window=5, threshold=25)
trim_packet2 = trim(trim_quality(trim_packet))
seq2 = trim_packet2[SEQS_PASSED][0][0]
assert get_int_qualities(seq2) == [40, 18, 10, 40, 40]
quals = [
40, 40, 13, 11, 40, 9, 40, 4, 27, 38, 40, 4, 11, 40, 40, 10, 10,
21, 3, 40, 9, 9, 12, 10, 9
]
seq = SeqRecord(Seq('atatatatatatatatatatatata'))
seq.letter_annotations['phred_quality'] = quals
seq = SeqWrapper(SEQRECORD, seq, None)
trim_quality = TrimByQuality(window=5, threshold=25)
trim_packet = {SEQS_PASSED: [[seq]], ORPHAN_SEQS: []}
trim_packet2 = trim(trim_quality(trim_packet))
seq2 = trim_packet2[SEQS_PASSED][0][0]
expected = [40, 4, 27, 38, 40]
assert get_int_qualities(seq2) == expected
quals = [
40, 40, 13, 11, 40, 9, 40, 4, 27, 38, 40, 4, 11, 40, 40, 10, 10,
21, 3, 40, 9, 9, 12, 10, 9
]
seq = SeqRecord(Seq('atatatatatatatatatatatata'))
seq.letter_annotations['phred_quality'] = quals
seq = SeqWrapper(SEQRECORD, seq, None)
trim_packet = {SEQS_PASSED: [[seq]], ORPHAN_SEQS: []}
trim_quality = TrimByQuality(window=5, threshold=25, trim_left=False)
trim_packet2 = trim(trim_quality(trim_packet))
seq2 = trim_packet2[SEQS_PASSED][0][0]
assert get_int_qualities(seq2) == [
40, 40, 13, 11, 40, 9, 40, 4, 27, 38, 40
]
quals = [
40, 40, 13, 11, 40, 9, 40, 4, 27, 38, 40, 4, 11, 40, 40, 10, 10,
21, 3, 40, 9, 9, 12, 10, 9
]
seq = SeqRecord(Seq('atatatatatatatatatatatata'))
seq.letter_annotations['phred_quality'] = quals
seq = SeqWrapper(SEQRECORD, seq, None)
trim_packet = {SEQS_PASSED: [[seq]], ORPHAN_SEQS: []}
trim_quality = TrimByQuality(window=5, threshold=25, trim_right=False)
trim_packet2 = trim(trim_quality(trim_packet))
seq2 = trim_packet2[SEQS_PASSED][0][0]
assert get_int_qualities(seq2) == [
40, 4, 27, 38, 40, 4, 11, 40, 40, 10, 10, 21, 3, 40, 9, 9, 12, 10,
9
]
quals = [
40, 40, 13, 11, 40, 9, 40, 4, 27, 38, 40, 4, 11, 40, 40, 10, 10,
21, 3, 40, 9, 9, 12, 10, 9
]
seq = SeqRecord(Seq('atatatatatatatatatatatata'))
seq.letter_annotations['phred_quality'] = quals
seq = SeqWrapper(SEQRECORD, seq, None)
trim_quality = TrimByQuality(window=5,
threshold=25,
trim_right=False,
trim_left=False)
trim_packet = {SEQS_PASSED: [[seq]], ORPHAN_SEQS: []}
trim_packet2 = trim(trim_quality(trim_packet))
seq2 = trim_packet2[SEQS_PASSED][0][0]
assert get_int_qualities(seq2) == quals
# With SeqItems
seq = SeqItem('s', [
'@s\n', 'atatatatatatatatatatatata\n', '\n',
'II.,I*I%<GI%,II++6$I**-+*\n'
])
seq = SeqWrapper(SEQITEM, seq, 'fastq')
trim_quality = TrimByQuality(window=5,
threshold=25,
trim_right=True,
trim_left=False)
trim_packet = {SEQS_PASSED: [[seq]], ORPHAN_SEQS: []}
trim_packet2 = trim(trim_quality(trim_packet))
seq2 = trim_packet2[SEQS_PASSED][0][0]
assert seq2.object.lines[3] == 'II.,I*I%<GI\n'
def _itemize_fastq_singleline(fhand):
'It returns the fhand divided in chunks, one per seq'
# group_in_packets_fill_last is faster than group_in_packets
blobs = group_in_packets_fill_last(ifilter(_line_is_not_empty, fhand), 4)
return (SeqItem(_get_name_from_lines(lines), lines) for lines in blobs)
