def match_pairs(reads,
out_fhand,
orphan_out_fhand,
out_format,
ordered=True,
check_order_buffer_size=0,
max_reads_memory=None,
temp_dir=None):
'''It matches the seq pairs in an iterator and splits the orphan seqs.'''
counts = 0
check_order_buffer = KeyedSet()
for pair in _get_paired_and_orphan(reads, ordered, max_reads_memory,
temp_dir):
if len(pair) == 1:
write_seqs(pair, orphan_out_fhand, out_format)
try:
name = _parse_pair_direction_and_name(pair[0])[0]
except PairDirectionError:
name = get_name(pair[0])
if ordered and counts < check_order_buffer_size:
counts += 1
if not check_order_buffer.check_add(name):
msg = 'Reads are not ordered by pairs.Use unordered option'
raise ItemsNotSortedError(msg)
elif ordered and counts >= check_order_buffer_size:
if name in check_order_buffer:
msg = 'Reads are not ordered by pairs.Use unordered option'
raise ItemsNotSortedError(msg)
elif len(pair) == 2:
write_seqs(pair, out_fhand, out_format)
flush_fhand(orphan_out_fhand)
flush_fhand(out_fhand)
def match_pairs(reads, out_fhand, orphan_out_fhand, out_format, ordered=True,
check_order_buffer_size=0, max_reads_memory=None,
temp_dir=None):
'''It matches the seq pairs in an iterator and splits the orphan seqs.'''
counts = 0
check_order_buffer = KeyedSet()
for pair in _get_paired_and_orphan(reads, ordered, max_reads_memory,
temp_dir):
if len(pair) == 1:
write_seqs(pair, orphan_out_fhand, out_format)
try:
name = _parse_pair_direction_and_name(pair[0])[0]
except PairDirectionError:
name = get_name(pair[0])
if ordered and counts < check_order_buffer_size:
counts += 1
if not check_order_buffer.check_add(name):
msg = 'Reads are not ordered by pairs.Use unordered option'
raise ItemsNotSortedError(msg)
elif ordered and counts >= check_order_buffer_size:
if name in check_order_buffer:
msg = 'Reads are not ordered by pairs.Use unordered option'
raise ItemsNotSortedError(msg)
elif len(pair) == 2:
write_seqs(pair, out_fhand, out_format)
flush_fhand(orphan_out_fhand)
flush_fhand(out_fhand)
def deinterleave_pairs(seqs, out_fhand1, out_fhand2, out_format):
'''It splits a sequence iterator with alternating paired reads in two.
It will fail if forward and reverse reads are not alternating.
'''
for pair in group_pairs(seqs, n_seqs_in_pair=2):
write_seqs((pair[0], ), out_fhand1, out_format)
write_seqs((pair[1], ), out_fhand2, out_format)
out_fhand1.flush()
out_fhand2.flush()
def deinterleave_pairs(seqs, out_fhand1, out_fhand2, out_format):
'''It splits a sequence iterator with alternating paired reads in two.
It will fail if forward and reverse reads are not alternating.
'''
for pair in group_pairs(seqs, n_seqs_in_pair=2):
write_seqs((pair[0],), out_fhand1, out_format)
write_seqs((pair[1],), out_fhand2, out_format)
out_fhand1.flush()
out_fhand2.flush()
def _pre_trim(self, trim_packet):
seqs = [s for seqs in trim_packet[SEQS_PASSED]for s in seqs]
reads_fhand = NamedTemporaryFile(dir=self._tempdir, suffix='.trimming')
write_seqs(seqs, reads_fhand)
reads_fhand.flush()
bwa = map_with_bwamem(self._index_fpath,
interleave_fpath=reads_fhand.name)
bam_fhand = NamedTemporaryFile(dir=self._tempdir)
map_process_to_sortedbam(bwa, bam_fhand.name, key='queryname',
tempdir=self._tempdir)
self._bam_fhand = bam_fhand
reads_fhand.close()
def filter_duplicates(in_fhands, out_fhand, paired_reads, use_length=None,
n_seqs_packet=None, tempdir=None):
if not in_fhands:
raise ValueError('At least one input fhand is required')
pairs = _read_pairs(in_fhands, paired_reads)
get_pair_key = _PairKeyGetter(use_length=use_length)
if n_seqs_packet is None:
unique_pairs = unique_unordered(pairs, key=get_pair_key)
else:
sorted_pairs = sorted_items(pairs, key=get_pair_key, tempdir=tempdir,
max_items_in_memory=n_seqs_packet)
unique_pairs = unique(sorted_pairs, key=get_pair_key)
for pair in unique_pairs:
write_seqs(pair, out_fhand)
def __call__(self, seqs):
'It splits a list of sequences with the provided linkers'
seq_fhand = write_seqs(seqs, file_format='fasta')
seq_fhand.flush()
min_identity = 87.0
min_len = 13
filters = [{'kind': 'min_length', 'min_num_residues': min_len,
'length_in_query': False, 'filter_match_parts': True},
{'kind': 'score_threshold', 'score_key': 'identity',
'min_score': min_identity}]
matcher = BlasterForFewSubjects(seq_fhand.name, self.linkers,
program='blastn', filters=filters,
params={'task': 'blastn-short'},
elongate_for_global=True,
seqs_type=NUCL)
new_seqs = []
for seq in seqs:
segments = matcher.get_matched_segments_for_read(get_name(seq))
if segments is not None:
split_seqs = self._split_by_mate_linker(seq, segments)
else:
split_seqs = [seq]
for seq in split_seqs:
new_seqs.append(seq)
return new_seqs
def __call__(self, seqs):
'It splits a list of sequences with the provided linkers'
seq_fhand = write_seqs(seqs, file_format='fasta')
seq_fhand.flush()
min_identity = 87.0
min_len = 13
filters = [{
'kind': 'min_length',
'min_num_residues': min_len,
'length_in_query': False,
'filter_match_parts': True
}, {
'kind': 'score_threshold',
'score_key': 'identity',
'min_score': min_identity
}]
matcher = BlasterForFewSubjects(seq_fhand.name,
self.linkers,
program='blastn',
filters=filters,
params={'task': 'blastn-short'},
elongate_for_global=True,
seqs_type=NUCL)
new_seqs = []
for seq in seqs:
segments = matcher.get_matched_segments_for_read(get_name(seq))
if segments is not None:
split_seqs = self._split_by_mate_linker(seq, segments)
else:
split_seqs = [seq]
for seq in split_seqs:
new_seqs.append(seq)
return new_seqs
def _pre_trim(self, trim_packet):
seqs = [s for seqs in trim_packet[SEQS_PASSED] for s in seqs]
reads_fhand = NamedTemporaryFile(dir=self._tempdir, suffix='.trimming')
write_seqs(seqs, reads_fhand)
reads_fhand.flush()
bwa = map_with_bwamem(self._index_fpath,
interleave_fpath=reads_fhand.name)
bam_fhand = NamedTemporaryFile(dir=self._tempdir)
map_process_to_sortedbam(bwa,
bam_fhand.name,
key='queryname',
tempdir=self._tempdir)
self._bam_fhand = bam_fhand
reads_fhand.close()
def _do_blast_2(db_fpath,
queries,
program,
dbtype=None,
blast_format=None,
params=None,
remote=False):
'''It returns an alignment result with the blast.
It is an alternative interface to the one based on fpaths.
db_fpath should be a plain sequence file.
queries should be a SeqRecord list.
If an alternative blast output format is given it should be tabular, so
blast_format is a list of fields.
'''
query_fhand = write_seqs(queries, file_format='fasta')
query_fhand.flush()
if remote:
blastdb = db_fpath
fmt = 'XML' if blast_format is None else blast_format.upper()
else:
blastdb = get_or_create_blastdb(db_fpath, dbtype=dbtype)
if blast_format is None:
blast_format = [
'query',
'subject',
'query_length',
'subject_length',
'query_start',
'query_end',
'subject_start',
'subject_end',
'expect',
'identity',
]
fmt = generate_tabblast_format(blast_format)
if params is None:
params = {}
params['outfmt'] = fmt
blast_fhand = tempfile.NamedTemporaryFile(suffix='.blast')
do_blast(query_fhand.name,
blastdb,
program,
blast_fhand.name,
params,
remote=remote)
if remote:
blasts = BlastParser(blast_fhand)
else:
blasts = TabularBlastParser(blast_fhand, blast_format)
return blasts, blast_fhand
def filter_duplicates(in_fhands,
out_fhand,
paired_reads,
use_length=None,
n_seqs_packet=None,
tempdir=None):
if not in_fhands:
raise ValueError('At least one input fhand is required')
pairs = _read_pairs(in_fhands, paired_reads)
get_pair_key = _PairKeyGetter(use_length=use_length)
if n_seqs_packet is None:
unique_pairs = unique_unordered(pairs, key=get_pair_key)
else:
sorted_pairs = sorted_items(pairs,
key=get_pair_key,
tempdir=tempdir,
max_items_in_memory=n_seqs_packet)
unique_pairs = unique(sorted_pairs, key=get_pair_key)
for pair in unique_pairs:
write_seqs(pair, out_fhand)
def _run_estscan(seqs, pep_out_fpath, dna_out_fpath, matrix_fpath):
'It runs estscan in the input seqs'
seq_fhand = write_seqs(seqs, file_format='fasta')
seq_fhand.flush()
binary = get_binary_path('estscan')
cmd = [binary, '-t', pep_out_fpath, '-o', dna_out_fpath, '-M',
matrix_fpath, seq_fhand.name]
process = popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
check_process_finishes(process, binary=cmd[0])
seq_fhand.close()
def test_seqitems_io(self):
'It checks the different seq class streams IO'
fhand = StringIO('>s1\nACTG\n>s2 desc\nACTG\n')
seqs = list(read_seqs([fhand], prefered_seq_classes=[SEQITEM]))
assert seqs[0].kind == SEQITEM
fhand = StringIO()
write_seqs(seqs, fhand)
assert fhand.getvalue() == '>s1\nACTG\n>s2 desc\nACTG\n'
assert seqs[0].object.name == 's1'
# SeqRecord
fhand = StringIO('>s1\nACTG\n>s2 desc\nACTG\n')
seqs = list(read_seqs([fhand], prefered_seq_classes=[SEQRECORD]))
assert seqs[0].kind == SEQRECORD
fhand = StringIO()
write_seqs(seqs, fhand, 'fasta')
assert fhand.getvalue() == '>s1\nACTG\n>s2 desc\nACTG\n'
# seqitem not possible with different input and output formats
fhand = StringIO('>s1\nACTG\n>s2 desc\nACTG\n')
try:
seqs = list(read_seqs([fhand], out_format='fastq',
prefered_seq_classes=[SEQITEM]))
self.fail('ValueError expected')
except ValueError:
pass
fhand = StringIO('>s1\nACTG\n>s2 desc\nACTG\n')
seqs = list(read_seqs([fhand], out_format='fasta',
prefered_seq_classes=[SEQITEM]))
fhand = StringIO()
write_seqs(seqs, fhand)
assert fhand.getvalue() == '>s1\nACTG\n>s2 desc\nACTG\n'
def _setup_checks(self, filterpacket):
index_fpath = self._index_fpath
seqs = [s for seqs in filterpacket[SEQS_PASSED] for s in seqs]
seq_class = seqs[0].kind
extra_params = []
# Which format do we need for the bowtie2 input read file fasta or
# fastq?
if seq_class == SEQRECORD:
if 'phred_quality' in seqs[0].object.letter_annotations.viewkeys():
file_format = 'fastq'
else:
extra_params.append('-f')
file_format = 'fasta'
elif seq_class == SEQITEM:
file_format = get_file_format(seqs[0])
if 'illumina' in file_format:
extra_params.append('--phred64')
elif 'fasta' in file_format:
extra_params.append('-f')
elif 'fastq' in file_format:
pass
else:
msg = 'For FilterBowtie2Match and SeqItems fastq or fasta '
msg += 'files are required'
raise RuntimeError(msg)
else:
raise NotImplementedError()
reads_fhand = NamedTemporaryFile(suffix=file_format)
write_seqs(seqs, reads_fhand, file_format=file_format)
reads_fhand.flush()
bam_fhand = NamedTemporaryFile(suffix='.bam')
map_process = map_with_bowtie2(index_fpath,
unpaired_fpath=reads_fhand.name,
extra_params=extra_params,
threads=self.threads)
map_process_to_bam(map_process, bam_fhand.name)
self.mapped_reads = _get_mapped_reads(bam_fhand.name, self.min_mapq)
def _setup_checks(self, filterpacket):
index_fpath = self._index_fpath
seqs = [s for seqs in filterpacket[SEQS_PASSED]for s in seqs]
seq_class = seqs[0].kind
extra_params = []
# Which format do we need for the bowtie2 input read file fasta or
# fastq?
if seq_class == SEQRECORD:
if 'phred_quality' in seqs[0].object.letter_annotations.viewkeys():
file_format = 'fastq'
else:
extra_params.append('-f')
file_format = 'fasta'
elif seq_class == SEQITEM:
file_format = get_file_format(seqs[0])
if 'illumina' in file_format:
extra_params.append('--phred64')
elif 'fasta' in file_format:
extra_params.append('-f')
elif 'fastq' in file_format:
pass
else:
msg = 'For FilterBowtie2Match and SeqItems fastq or fasta '
msg += 'files are required'
raise RuntimeError(msg)
else:
raise NotImplementedError()
reads_fhand = NamedTemporaryFile(suffix=file_format)
write_seqs(seqs, reads_fhand, file_format=file_format)
reads_fhand.flush()
bam_fhand = NamedTemporaryFile(suffix='.bam')
map_process = map_with_bowtie2(index_fpath,
unpaired_fpath=reads_fhand.name,
extra_params=extra_params,
threads=self.threads)
map_process_to_bam(map_process, bam_fhand.name)
self.mapped_reads = _get_mapped_reads(bam_fhand.name, self.min_mapq)
def classify_chimeras(in_fhand,
index_fpath,
mate_distance,
out_fhand,
chimeras_fhand=None,
unknown_fhand=None,
tempdir=None,
threads=None,
settings=get_setting('CHIMERAS_SETTINGS')):
'''It maps sequences from input files, sorts them and writes to output
files according to its classification'''
bam_fhand = NamedTemporaryFile(suffix='.bam')
extra_params = ['-a', '-M']
bwa = map_with_bwamem(index_fpath,
interleave_fpath=in_fhand.name,
extra_params=extra_params)
map_process_to_sortedbam(bwa,
bam_fhand.name,
key='queryname',
tempdir=tempdir)
for pair, kind in classify_mapped_reads(bam_fhand,
settings=settings,
mate_distance=mate_distance):
if kind is NON_CHIMERIC:
write_seqs(pair, out_fhand)
elif kind is CHIMERA and chimeras_fhand is not None:
write_seqs(pair, chimeras_fhand)
elif kind is UNKNOWN and unknown_fhand is not None:
write_seqs(pair, unknown_fhand)
def _run_estscan(seqs, pep_out_fpath, dna_out_fpath, matrix_fpath):
'It runs estscan in the input seqs'
seq_fhand = write_seqs(seqs, file_format='fasta')
seq_fhand.flush()
binary = get_binary_path('estscan')
cmd = [
binary, '-t', pep_out_fpath, '-o', dna_out_fpath, '-M', matrix_fpath,
seq_fhand.name
]
process = popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
check_process_finishes(process, binary=cmd[0])
seq_fhand.close()
def _pre_trim(self, trim_packet):
seqs = [s for seqs in trim_packet[SEQS_PASSED]for s in seqs]
db_fhand = write_seqs(seqs, file_format='fasta')
db_fhand.flush()
params = {'task': 'blastn-short', 'expect': '0.0001'}
filters = [{'kind': 'score_threshold', 'score_key': 'identity',
'min_score': 87},
{'kind': 'min_length', 'min_num_residues': 13,
'length_in_query': False}]
self._matcher = BlasterForFewSubjects(db_fhand.name, self.oligos,
program='blastn', filters=filters,
params=params,
elongate_for_global=True)
def _setup_checks(self, filterpacket):
seqs = [s for seqs in filterpacket[SEQS_PASSED]for s in seqs]
# we create a blastdb for these reads and then we use the oligos
# as the blast query
db_fhand = write_seqs(seqs, file_format='fasta')
db_fhand.flush()
params = {'task': 'blastn-short', 'expect': '0.0001'}
filters = [{'kind': 'score_threshold', 'score_key': 'identity',
'min_score': 87},
{'kind': 'min_length', 'min_num_residues': 13,
'length_in_query': False}]
self._matcher = BlasterForFewSubjects(db_fhand.name, self.oligos,
program='blastn', filters=filters,
params=params,
elongate_for_global=False)
def _pre_trim(self, trim_packet):
seqs = [s for seqs in trim_packet[SEQS_PASSED] for s in seqs]
db_fhand = write_seqs(seqs, file_format='fasta')
db_fhand.flush()
params = {'task': 'blastn-short', 'expect': '0.0001'}
filters = [{
'kind': 'score_threshold',
'score_key': 'identity',
'min_score': 87
}, {
'kind': 'min_length',
'min_num_residues': 13,
'length_in_query': False
}]
self._matcher = BlasterForFewSubjects(db_fhand.name,
self.oligos,
program='blastn',
filters=filters,
params=params,
elongate_for_global=True)
def _do_blast_2(db_fpath, queries, program, dbtype=None, blast_format=None,
params=None, remote=False):
'''It returns an alignment result with the blast.
It is an alternative interface to the one based on fpaths.
db_fpath should be a plain sequence file.
queries should be a SeqRecord list.
If an alternative blast output format is given it should be tabular, so
blast_format is a list of fields.
'''
query_fhand = write_seqs(queries, file_format='fasta')
query_fhand.flush()
if remote:
blastdb = db_fpath
fmt = 'XML' if blast_format is None else blast_format.upper()
else:
blastdb = get_or_create_blastdb(db_fpath, dbtype=dbtype)
if blast_format is None:
blast_format = ['query', 'subject', 'query_length', 'subject_length',
'query_start', 'query_end', 'subject_start',
'subject_end', 'expect', 'identity', ]
fmt = generate_tabblast_format(blast_format)
if params is None:
params = {}
params['outfmt'] = fmt
blast_fhand = tempfile.NamedTemporaryFile(suffix='.blast')
do_blast(query_fhand.name, blastdb, program, blast_fhand.name, params,
remote=remote)
if remote:
blasts = BlastParser(blast_fhand)
else:
blasts = TabularBlastParser(blast_fhand, blast_format)
return blasts, blast_fhand
def _setup_checks(self, filterpacket):
seqs = [s for seqs in filterpacket[SEQS_PASSED] for s in seqs]
# we create a blastdb for these reads and then we use the oligos
# as the blast query
db_fhand = write_seqs(seqs, file_format='fasta')
db_fhand.flush()
params = {'task': 'blastn-short', 'expect': '0.0001'}
filters = [{
'kind': 'score_threshold',
'score_key': 'identity',
'min_score': 87
}, {
'kind': 'min_length',
'min_num_residues': 13,
'length_in_query': False
}]
self._matcher = BlasterForFewSubjects(db_fhand.name,
self.oligos,
program='blastn',
filters=filters,
params=params,
elongate_for_global=False)
def classify_chimeras(in_fhand, index_fpath, mate_distance, out_fhand,
chimeras_fhand=None, unknown_fhand=None, tempdir=None,
threads=None, settings=get_setting('CHIMERAS_SETTINGS')):
'''It maps sequences from input files, sorts them and writes to output
files according to its classification'''
bam_fhand = NamedTemporaryFile(suffix='.bam')
extra_params = ['-a', '-M']
bwa = map_with_bwamem(index_fpath, interleave_fpath=in_fhand.name,
extra_params=extra_params)
map_process_to_sortedbam(bwa, bam_fhand.name, key='queryname',
tempdir=tempdir)
for pair, kind in classify_mapped_reads(bam_fhand, settings=settings,
mate_distance=mate_distance):
if kind is NON_CHIMERIC:
write_seqs(pair, out_fhand)
elif kind is CHIMERA and chimeras_fhand is not None:
write_seqs(pair, chimeras_fhand)
elif kind is UNKNOWN and unknown_fhand is not None:
write_seqs(pair, unknown_fhand)
def test_seqitems_io(self):
'It checks the different seq class streams IO'
fhand = StringIO('>s1\nACTG\n>s2 desc\nACTG\n')
seqs = list(read_seqs([fhand], prefered_seq_classes=[SEQITEM]))
assert seqs[0].kind == SEQITEM
fhand = StringIO()
write_seqs(seqs, fhand)
assert fhand.getvalue() == '>s1\nACTG\n>s2 desc\nACTG\n'
assert seqs[0].object.name == 's1'
# SeqRecord
fhand = StringIO('>s1\nACTG\n>s2 desc\nACTG\n')
seqs = list(read_seqs([fhand], prefered_seq_classes=[SEQRECORD]))
assert seqs[0].kind == SEQRECORD
fhand = StringIO()
write_seqs(seqs, fhand, 'fasta')
assert fhand.getvalue() == '>s1\nACTG\n>s2 desc\nACTG\n'
# seqitem not possible with different input and output formats
fhand = StringIO('>s1\nACTG\n>s2 desc\nACTG\n')
try:
seqs = list(
read_seqs([fhand],
out_format='fastq',
prefered_seq_classes=[SEQITEM]))
self.fail('ValueError expected')
except ValueError:
pass
fhand = StringIO('>s1\nACTG\n>s2 desc\nACTG\n')
seqs = list(
read_seqs([fhand],
out_format='fasta',
prefered_seq_classes=[SEQITEM]))
fhand = StringIO()
write_seqs(seqs, fhand)
assert fhand.getvalue() == '>s1\nACTG\n>s2 desc\nACTG\n'
