def permuted_copy(self, partition=None):
""" Return a copy of the collection with all alignment columns permuted
"""
def take(n, iterable):
return [iterable.next() for _ in range(n)]
if partition is None:
partition = Partition([1] * len(self))
index_tuples = partition.get_membership()
alignments = []
for ix in index_tuples:
concat = Concatenation(self, ix)
sites = concat.alignment.get_sites()
random.shuffle(sites)
d = dict(zip(concat.alignment.get_names(), [iter(x) for x in zip(*sites)]))
new_seqs = [[(k, ''.join(take(l, d[k]))) for k in d] for l in concat.lengths]
for seqs, datatype, name in zip(new_seqs, concat.datatypes, concat.names):
alignment = Alignment(seqs, datatype)
alignment.name = name
alignments.append(alignment)
return self.__class__(records=sorted(alignments, key=lambda x: SORT_KEY(x.name)))
def permuted_copy(self, partition=None):
""" Return a copy of the collection with all alignment columns permuted
"""
def take(n, iterable):
return [iterable.next() for _ in range(n)]
if partition is None:
partition = Partition([1] * len(self))
index_tuples = partition.get_membership()
alignments = []
for ix in index_tuples:
concat = Concatenation(self, ix)
sites = concat.alignment.get_sites()
random.shuffle(sites)
d = dict(
zip(concat.alignment.get_names(),
[iter(x) for x in zip(*sites)]))
new_seqs = [[(k, ''.join(take(l, d[k]))) for k in d]
for l in concat.lengths]
for seqs, datatype, name in zip(new_seqs, concat.datatypes,
concat.names):
alignment = Alignment(seqs, datatype)
alignment.name = name
alignments.append(alignment)
return self.__class__(
records=sorted(alignments, key=lambda x: SORT_KEY(x.name)))
def read_alignments(self, input_dir, file_format, header_grep=None, compression=None):
""" Get list of alignment files from an input directory *.fa, *.fas and
*.phy files only
Stores in self.files """
optioncheck(compression, [None, 'gz', 'bz2'])
if file_format == 'fasta':
extensions = ['fa', 'fas', 'fasta']
elif file_format == 'phylip':
extensions = ['phy']
else:
extensions = []
if compression:
extensions = ['.'.join([x, compression]) for x in extensions]
files = fileIO.glob_by_extensions(input_dir, extensions)
files.sort(key=SORT_KEY)
self._input_files = files
records = []
pbar = setup_progressbar("Loading files", len(files), simple_progress=True)
pbar.start()
for i, f in enumerate(files):
if compression is not None:
with fileIO.TempFile() as tmpfile:
with fileIO.freader(f, compression) as reader, fileIO.fwriter(tmpfile) as writer:
for line in reader:
writer.write(line)
try:
record = Alignment(tmpfile, file_format, True)
except RuntimeError:
record = Alignment(tmpfile, file_format, False)
else:
try:
record = Alignment(f, file_format, True)
except RuntimeError:
record = Alignment(f, file_format, False)
if header_grep:
try:
datatype = 'dna' if record.is_dna() else 'protein'
record = Alignment([(header_grep(x), y) for (x, y) in record.get_sequences()], datatype)
except TypeError:
raise TypeError("Couldn't apply header_grep to header\n"
"alignment number={}, name={}\n"
"header_grep={}".format(i, fileIO.strip_extensions(f), header_grep))
except RuntimeError:
print('RuntimeError occurred processing alignment number={}, name={}'
.format(i, fileIO.strip_extensions(f)))
raise
record.name = (fileIO.strip_extensions(f))
records.append(record)
pbar.update(i)
pbar.finish()
return records
def read_alignments(self,
input_dir,
file_format,
header_grep=None,
compression=None):
""" Get list of alignment files from an input directory *.fa, *.fas and
*.phy files only
Stores in self.files """
optioncheck(compression, [None, 'gz', 'bz2'])
if file_format == 'fasta':
extensions = ['fa', 'fas', 'fasta']
elif file_format == 'phylip':
extensions = ['phy']
else:
extensions = []
if compression:
extensions = ['.'.join([x, compression]) for x in extensions]
files = fileIO.glob_by_extensions(input_dir, extensions)
files.sort(key=SORT_KEY)
self._input_files = files
records = []
pbar = setup_progressbar("Loading files",
len(files),
simple_progress=True)
pbar.start()
for i, f in enumerate(files):
if compression is not None:
with fileIO.TempFile() as tmpfile:
with fileIO.freader(f,
compression) as reader, fileIO.fwriter(
tmpfile) as writer:
for line in reader:
writer.write(line)
try:
record = Alignment(tmpfile, file_format, True)
except RuntimeError:
record = Alignment(tmpfile, file_format, False)
else:
try:
record = Alignment(f, file_format, True)
except RuntimeError:
record = Alignment(f, file_format, False)
if header_grep:
try:
datatype = 'dna' if record.is_dna() else 'protein'
record = Alignment([(header_grep(x), y)
for (x, y) in record.get_sequences()],
datatype)
except TypeError:
raise TypeError("Couldn't apply header_grep to header\n"
"alignment number={}, name={}\n"
"header_grep={}".format(
i, fileIO.strip_extensions(f),
header_grep))
except RuntimeError:
print(
'RuntimeError occurred processing alignment number={}, name={}'
.format(i, fileIO.strip_extensions(f)))
raise
record.name = (fileIO.strip_extensions(f))
records.append(record)
pbar.update(i)
pbar.finish()
return records
