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 __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 _read_seqitems(fhands):
'it returns an iterator of seq items (tuples of name and chunk)'
seq_iters = []
for fhand in fhands:
file_format = get_format(fhand)
seq_iter = _itemize_fastx(fhand)
seq_iter = assing_kind_to_seqs(SEQITEM, seq_iter, file_format)
seq_iters.append(seq_iter)
return chain.from_iterable(seq_iters)
def _read_seqitems(fhands):
'it returns an iterator of seq items (tuples of name and chunk)'
seq_iters = []
for fhand in fhands:
file_format = get_format(fhand)
seq_iter = _itemize_fastx(fhand)
seq_iter = assing_kind_to_seqs(SEQITEM, seq_iter, file_format)
seq_iters.append(seq_iter)
return chain.from_iterable(seq_iters)
def test_case_change(self):
'It changes the case of the sequences'
seqs = [SeqRecord(Seq('aCCg'), letter_annotations={'dummy': 'dddd'})]
seqs = assing_kind_to_seqs(SEQRECORD, seqs, None)
change_case = ChangeCase(action=UPPERCASE)
strs = [get_str_seq(s) for s in change_case(seqs)]
assert strs == ['ACCG']
seqs = [SeqRecord(Seq('aCCg'))]
seqs = assing_kind_to_seqs(SEQRECORD, seqs, None)
change_case = ChangeCase(action=LOWERCASE)
strs = [get_str_seq(s) for s in change_case(seqs)]
assert strs == ['accg']
seqs = [SeqRecord(Seq('aCCg'))]
seqs = assing_kind_to_seqs(SEQRECORD, seqs, None)
change_case = ChangeCase(action=SWAPCASE)
strs = [get_str_seq(s) for s in change_case(seqs)]
assert strs == ['AccG']
def test_case_change(self):
'It changes the case of the sequences'
seqs = [SeqRecord(Seq('aCCg'), letter_annotations={'dummy': 'dddd'})]
seqs = assing_kind_to_seqs(SEQRECORD, seqs, None)
change_case = ChangeCase(action=UPPERCASE)
strs = [get_str_seq(s) for s in change_case(seqs)]
assert strs == ['ACCG']
seqs = [SeqRecord(Seq('aCCg'))]
seqs = assing_kind_to_seqs(SEQRECORD, seqs, None)
change_case = ChangeCase(action=LOWERCASE)
strs = [get_str_seq(s) for s in change_case(seqs)]
assert strs == ['accg']
seqs = [SeqRecord(Seq('aCCg'))]
seqs = assing_kind_to_seqs(SEQRECORD, seqs, None)
change_case = ChangeCase(action=SWAPCASE)
strs = [get_str_seq(s) for s in change_case(seqs)]
assert strs == ['AccG']
def test_matching_segments(self):
'It tests the detection of oligos in sequence files'
seq_5 = 'CTAGTCTAGTCGTAGTCATGGCTGTAGTCTAGTCTACGATTCGTATCAGTTGTGTGAC'
mate_fhand = create_a_matepair_file()
linkers = assing_kind_to_seqs(SEQRECORD, LINKERS, None)
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_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_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 _read_seqitems(fhands, file_format):
'it returns an iterator of seq items (tuples of name and chunk)'
seq_iters = []
for fhand in fhands:
if file_format == GUESS_FORMAT or file_format is None:
file_format = guess_format(fhand)
else:
file_format = file_format
if file_format == 'fasta':
seq_iter = _itemize_fasta(fhand)
elif 'multiline' not in file_format and 'fastq' in file_format:
seq_iter = _itemize_fastq(fhand)
else:
msg = 'Format not supported by the itemizers: ' + file_format
raise NotImplementedError(msg)
seq_iter = assing_kind_to_seqs(SEQITEM, seq_iter, file_format)
seq_iters.append(seq_iter)
return chain.from_iterable(seq_iters)
def read_seqs(fhands,
file_format=GUESS_FORMAT,
out_format=None,
prefered_seq_classes=None):
'It returns a stream of seqs in different codings: seqrecords, seqitems...'
if not prefered_seq_classes:
prefered_seq_classes = [SEQITEM, SEQRECORD]
if file_format == GUESS_FORMAT:
in_format = guess_format(fhands[0])
else:
in_format = file_format
if out_format not in (None, GUESS_FORMAT):
if in_format != out_format:
if SEQITEM in prefered_seq_classes:
# seqitems is incompatible with different input and output
# formats
prefered_seq_classes.pop(prefered_seq_classes.index(SEQITEM))
if not prefered_seq_classes:
msg = 'No valid seq class left or prefered'
raise ValueError(msg)
for seq_class in prefered_seq_classes:
if seq_class == SEQITEM:
try:
return _read_seqitems(fhands, in_format)
except NotImplementedError:
continue
elif seq_class == SEQRECORD:
try:
seqs = _read_seqrecords(fhands, in_format)
return assing_kind_to_seqs(SEQRECORD, seqs, None)
except NotImplementedError:
continue
else:
raise ValueError('Unknown class for seq: ' + seq_class)
raise RuntimeError('We should not be here, fixme')
def _read_seqitems(fhands):
'it returns an iterator of seq items (tuples of name and chunk)'
seq_iters = []
for fhand in fhands:
file_format = get_format(fhand)
if file_format == 'fasta':
seq_iter = _itemize_fasta(fhand)
elif 'multiline' not in file_format and 'fastq' in file_format:
try:
seq_iter = _itemize_fastq(fhand)
except ValueError as error:
if error_quality_disagree(error):
raise MalformedFile(str(error))
raise
else:
msg = 'Format not supported by the itemizers: ' + file_format
raise NotImplementedError(msg)
seq_iter = assing_kind_to_seqs(SEQITEM, seq_iter, file_format)
seq_iters.append(seq_iter)
return chain.from_iterable(seq_iters)
def read_seqs(fhands, file_format=GUESS_FORMAT, out_format=None,
prefered_seq_classes=None):
'It returns a stream of seqs in different codings: seqrecords, seqitems...'
if not prefered_seq_classes:
prefered_seq_classes = [SEQITEM, SEQRECORD]
if file_format == GUESS_FORMAT:
in_format = guess_format(fhands[0])
else:
in_format = file_format
if out_format not in (None, GUESS_FORMAT):
if in_format != out_format:
if SEQITEM in prefered_seq_classes:
# seqitems is incompatible with different input and output
# formats
prefered_seq_classes.pop(prefered_seq_classes.index(SEQITEM))
if not prefered_seq_classes:
msg = 'No valid seq class left or prefered'
raise ValueError(msg)
for seq_class in prefered_seq_classes:
if seq_class == SEQITEM:
try:
return _read_seqitems(fhands, in_format)
except NotImplementedError:
continue
elif seq_class == SEQRECORD:
try:
seqs = _read_seqrecords(fhands, in_format)
return assing_kind_to_seqs(SEQRECORD, seqs, None)
except NotImplementedError:
continue
else:
raise ValueError('Unknown class for seq: ' + seq_class)
raise RuntimeError('We should not be here, fixme')
def read_seqs(fhands, out_format=None, prefered_seq_classes=None):
'It returns a stream of seqs in different codings: seqrecords, seqitems...'
if not prefered_seq_classes:
prefered_seq_classes = [SEQITEM, SEQRECORD]
try:
in_format = get_format(fhands[0])
except FileIsEmptyError:
return []
# seqitems is incompatible with different input and output formats
# or when in_format != a fasta or fastq
if ((out_format not in (None, GUESS_FORMAT) and in_format != out_format
and SEQITEM in prefered_seq_classes) or
(in_format not in ('fasta',) + SANGER_FASTQ_FORMATS +
ILLUMINA_FASTQ_FORMATS)):
prefered_seq_classes.pop(prefered_seq_classes.index(SEQITEM))
if not prefered_seq_classes:
msg = 'No valid seq class left or prefered'
raise ValueError(msg)
for seq_class in prefered_seq_classes:
if seq_class == SEQITEM:
try:
return _read_seqitems(fhands)
except NotImplementedError:
continue
elif seq_class == SEQRECORD:
try:
seqs = _read_seqrecords(fhands)
return assing_kind_to_seqs(SEQRECORD, seqs, None)
except NotImplementedError:
continue
else:
raise ValueError('Unknown class for seq: ' + seq_class)
raise RuntimeError('We should not be here, fixme')
def read_seqs(fhands, out_format=None, prefered_seq_classes=None):
'It returns a stream of seqs in different codings: seqrecords, seqitems...'
if not prefered_seq_classes:
prefered_seq_classes = [SEQITEM, SEQRECORD]
try:
in_format = get_format(fhands[0])
except FileIsEmptyError:
return []
# seqitems is incompatible with different input and output formats
# or when in_format != a fasta or fastq
if ((out_format not in (None, GUESS_FORMAT) and in_format != out_format
and SEQITEM in prefered_seq_classes) or
(in_format not in ('fasta',) + SANGER_FASTQ_FORMATS +
ILLUMINA_FASTQ_FORMATS)):
prefered_seq_classes.pop(prefered_seq_classes.index(SEQITEM))
if not prefered_seq_classes:
msg = 'No valid seq class left or prefered'
raise ValueError(msg)
for seq_class in prefered_seq_classes:
if seq_class == SEQITEM:
try:
return _read_seqitems(fhands)
except NotImplementedError:
continue
elif seq_class == SEQRECORD:
try:
seqs = _read_seqrecords(fhands)
return assing_kind_to_seqs(SEQRECORD, seqs, None)
except NotImplementedError:
continue
else:
raise ValueError('Unknown class for seq: ' + seq_class)
raise RuntimeError('We should not be here, fixme')
def _read_seqitems(fhands, file_format):
'it returns an iterator of seq items (tuples of name and chunk)'
seq_iters = []
for fhand in fhands:
if file_format == GUESS_FORMAT or file_format is None:
file_format = guess_format(fhand)
else:
file_format = file_format
if file_format == 'fasta':
seq_iter = _itemize_fasta(fhand)
elif 'multiline' not in file_format and 'fastq' in file_format:
try:
seq_iter = _itemize_fastq(fhand)
except ValueError as error:
if error_quality_disagree(error):
raise MalformedFile(str(error))
raise
else:
msg = 'Format not supported by the itemizers: ' + file_format
raise NotImplementedError(msg)
seq_iter = assing_kind_to_seqs(SEQITEM, seq_iter, file_format)
seq_iters.append(seq_iter)
return chain.from_iterable(seq_iters)