def _alignment_to_phylip(obj, fh):
if obj.is_empty():
raise PhylipFormatError(
"Alignment can only be written in PHYLIP format if there is at "
"least one sequence in the alignment.")
sequence_length = obj.sequence_length()
if sequence_length == 0:
raise PhylipFormatError(
"Alignment can only be written in PHYLIP format if there is at "
"least one position in the alignment.")
chunk_size = 10
for id_ in obj.ids():
if len(id_) > chunk_size:
raise PhylipFormatError(
"Alignment can only be written in PHYLIP format if all "
"sequence IDs have %d or fewer characters. Found sequence "
"with ID '%s' that exceeds this limit. Use "
"Alignment.update_ids to assign shorter IDs." %
(chunk_size, id_))
sequence_count = obj.sequence_count()
fh.write('{0:d} {1:d}\n'.format(sequence_count, sequence_length))
fmt = '{0:%d}{1}\n' % chunk_size
for seq in obj:
chunked_seq = _chunk_str(str(seq), chunk_size, ' ')
fh.write(fmt.format(seq.metadata['id'], chunked_seq))
def _alignment_to_phylip(obj, fh):
if obj.is_empty():
raise PhylipFormatError(
"Alignment can only be written in PHYLIP format if there is at "
"least one sequence in the alignment.")
sequence_length = obj.sequence_length()
if sequence_length == 0:
raise PhylipFormatError(
"Alignment can only be written in PHYLIP format if there is at "
"least one position in the alignment.")
chunk_size = 10
for id_ in obj.ids():
if len(id_) > chunk_size:
raise PhylipFormatError(
"Alignment can only be written in PHYLIP format if all "
"sequence IDs have %d or fewer characters. Found sequence "
"with ID '%s' that exceeds this limit. Use "
"Alignment.update_ids to assign shorter IDs." %
(chunk_size, id_))
sequence_count = obj.sequence_count()
fh.write('{0:d} {1:d}\n'.format(sequence_count, sequence_length))
fmt = '{0:%d}{1}\n' % chunk_size
for seq in obj:
chunked_seq = _chunk_str(str(seq), chunk_size, ' ')
fh.write(fmt.format(seq.id, chunked_seq))
def _generator_to_fasta(obj, fh, qual=FileSentinel,
id_whitespace_replacement='_',
description_newline_replacement=' ', max_width=None):
if max_width is not None:
if max_width < 1:
raise ValueError(
"Maximum line width must be greater than zero (max_width=%d)."
% max_width)
if qual is not None:
# define text wrapper for splitting quality scores here for
# efficiency. textwrap docs recommend reusing a TextWrapper
# instance when it is used many times. configure text wrapper to
# never break "words" (i.e., integer quality scores) across lines
qual_wrapper = textwrap.TextWrapper(
width=max_width, break_long_words=False,
break_on_hyphens=False)
formatted_records = _format_fasta_like_records(
obj, id_whitespace_replacement, description_newline_replacement,
qual is not None)
for header, seq_str, qual_scores in formatted_records:
if max_width is not None:
seq_str = _chunk_str(seq_str, max_width, '\n')
fh.write('>%s\n%s\n' % (header, seq_str))
if qual is not None:
qual_str = ' '.join(np.asarray(qual_scores, dtype=np.str))
if max_width is not None:
qual_str = qual_wrapper.fill(qual_str)
qual.write('>%s\n%s\n' % (header, qual_str))
def _generator_to_fasta(obj, fh, qual=FileSentinel,
id_whitespace_replacement='_',
description_newline_replacement=' ', max_width=None):
if max_width is not None:
if max_width < 1:
raise ValueError(
"Maximum line width must be greater than zero (max_width=%d)."
% max_width)
if qual is not None:
# define text wrapper for splitting quality scores here for
# efficiency. textwrap docs recommend reusing a TextWrapper
# instance when it is used many times. configure text wrapper to
# never break "words" (i.e., integer quality scores) across lines
qual_wrapper = textwrap.TextWrapper(
width=max_width, break_long_words=False,
break_on_hyphens=False)
formatted_records = _format_fasta_like_records(
obj, id_whitespace_replacement, description_newline_replacement,
qual is not None)
for header, seq_str, qual_scores in formatted_records:
if max_width is not None:
seq_str = _chunk_str(seq_str, max_width, '\n')
fh.write('>%s\n%s\n' % (header, seq_str))
if qual is not None:
qual_str = ' '.join(np.asarray(qual_scores, dtype=np.str))
if max_width is not None:
qual_str = qual_wrapper.fill(qual_str)
qual.write('>%s\n%s\n' % (header, qual_str))
def test_even_split(self):
self.assertEqual(_chunk_str('abcdef', 6, ' '), 'abcdef')
self.assertEqual(_chunk_str('abcdef', 3, ' '), 'abc def')
self.assertEqual(_chunk_str('abcdef', 2, ' '), 'ab cd ef')
self.assertEqual(_chunk_str('abcdef', 1, ' '), 'a b c d e f')
self.assertEqual(_chunk_str('a', 1, ' '), 'a')
self.assertEqual(_chunk_str('abcdef', 2, ''), 'abcdef')
def test_even_split(self):
self.assertEqual(_chunk_str('abcdef', 6, ' '), 'abcdef')
self.assertEqual(_chunk_str('abcdef', 3, ' '), 'abc def')
self.assertEqual(_chunk_str('abcdef', 2, ' '), 'ab cd ef')
self.assertEqual(_chunk_str('abcdef', 1, ' '), 'a b c d e f')
self.assertEqual(_chunk_str('a', 1, ' '), 'a')
self.assertEqual(_chunk_str('abcdef', 2, ''), 'abcdef')
def _generator_to_fasta(obj, fh, id_whitespace_replacement='_',
description_newline_replacement=' ', max_width=None):
if ((id_whitespace_replacement is not None and
'\n' in id_whitespace_replacement) or
(description_newline_replacement is not None and
'\n' in description_newline_replacement)):
raise FASTAFormatError(
"Newline character (\\n) cannot be used to replace whitespace in "
"biological sequence IDs, nor to replace newlines in biological "
"sequence descriptions. Otherwise, the FASTA-formatted file will "
"be invalid.")
ws_pattern = re.compile(r'\s')
nl_pattern = re.compile(r'\n')
for idx, seq in enumerate(obj):
if len(seq) < 1:
raise FASTAFormatError(
"Cannot write %s biological sequence in FASTA format because "
"it does not contain any characters (i.e., it is an "
"empty/blank sequence). Empty sequences are not supported in "
"the FASTA file format." % cardinal_to_ordinal(idx + 1))
id_ = seq.id
if id_whitespace_replacement is not None:
id_ = re.sub(ws_pattern, id_whitespace_replacement, id_)
desc = seq.description
if description_newline_replacement is not None:
desc = re.sub(nl_pattern, description_newline_replacement, desc)
if desc:
header = '%s %s' % (id_, desc)
else:
header = id_
seq_str = str(seq)
if max_width is not None:
seq_str = _chunk_str(seq_str, max_width, '\n')
fh.write('>%s\n%s\n' % (header, seq_str))
def test_invalid_n(self):
with self.assertRaisesRegexp(ValueError, 'n=0'):
_chunk_str('abcdef', 0, ' ')
with self.assertRaisesRegexp(ValueError, 'n=-42'):
_chunk_str('abcdef', -42, ' ')
def test_uneven_split(self):
self.assertEqual(_chunk_str('abcdef', 5, '|'), 'abcde|f')
self.assertEqual(_chunk_str('abcdef', 4, '|'), 'abcd|ef')
self.assertEqual(_chunk_str('abcdefg', 3, ' - '), 'abc - def - g')
def test_no_split(self):
self.assertEqual(_chunk_str('', 2, '\n'), '')
self.assertEqual(_chunk_str('a', 100, '\n'), 'a')
self.assertEqual(_chunk_str('abcdef', 42, '|'), 'abcdef')
def test_invalid_n(self):
with self.assertRaisesRegexp(ValueError, 'n=0'):
_chunk_str('abcdef', 0, ' ')
with self.assertRaisesRegexp(ValueError, 'n=-42'):
_chunk_str('abcdef', -42, ' ')
def test_uneven_split(self):
self.assertEqual(_chunk_str('abcdef', 5, '|'), 'abcde|f')
self.assertEqual(_chunk_str('abcdef', 4, '|'), 'abcd|ef')
self.assertEqual(_chunk_str('abcdefg', 3, ' - '), 'abc - def - g')
def test_no_split(self):
self.assertEqual(_chunk_str('', 2, '\n'), '')
self.assertEqual(_chunk_str('a', 100, '\n'), 'a')
self.assertEqual(_chunk_str('abcdef', 42, '|'), 'abcdef')
