def fasta(self):
"""Make a fasta file with all uniprot proteins that are related to
this family."""
fasta = FASTA(self.p.proteins)
if not fasta.exists:
fasta.create()
for seq in pfam.fasta:
if self.fam_name in seq.description: fasta.add_seq(seq)
fasta.close()
assert fasta
# Return #
return fasta
def fasta(self):
"""Make a fasta file with all uniprot proteins that are related to
this family."""
fasta = FASTA(self.p.proteins)
if not fasta.exists:
fasta.create()
for seq in pfam.fasta:
if self.fam_name in seq.description: fasta.add_seq(seq)
fasta.close()
assert fasta
# Return #
return fasta
class PairedFASTA(object):
"""Read and write FASTA file pairs without using too much RAM"""
format = 'fasta'
def __len__(self):
return self.count
def __iter__(self):
return self.parse()
def __nonzero__(self):
return bool(self.fwd) and bool(self.rev)
def __repr__(self): return '<%s object on "%s" and "%s">' % \
(self.__class__.__name__, self.fwd.path, self.rev.path)
def __enter__(self):
return self.create()
def __exit__(self, exc_type, exc_value, traceback):
self.close()
@property
def exists(self):
return self.fwd.exists and self.rev.exists
def __init__(self, fwd, rev, parent=None):
# FASTA objects #
self.fwd = FASTA(fwd)
self.rev = FASTA(rev)
# Extra #
self.gzipped = self.fwd.gzipped
self.parent = parent
@property_cached
def count(self):
assert self.fwd.count == self.rev.count
return self.fwd.count
def open(self):
self.fwd.open()
self.rev.open()
def parse(self):
return izip(self.fwd.parse(), self.rev.parse())
def close(self):
self.fwd.close()
self.rev.close()
def create(self):
self.fwd.create()
self.rev.create()
return self
def add(self, f, r):
return self.add_pair((f, r))
def add_pair(self, pair):
self.fwd.add_seq(pair[0])
self.rev.add_seq(pair[1])
def remove(self):
self.fwd.remove()
self.rev.remove()
@property
def progress(self):
"""Just like self.parse but display a progress bar"""
return tqdm(self, total=len(self))
def subsample(self, down_to, dest_pair=None):
# Check size #
assert down_to < len(self)
# Make new pair of files #
if dest_pair is None:
dest_fwd_path = self.fwd_path.new_name_insert("subsampled")
dest_rev_path = self.rev_path.new_name_insert("subsampled")
dest_pair = self.__class__(dest_fwd_path, dest_rev_path)
# Do it #
dest_pair.create()
for pair in isubsample(self, down_to):
dest_pair.add_pair(pair)
self.subsampled.close()
# Did it work #
assert len(dest_pair) == down_to
#------------------------------- Extensions ------------------------------#
def parse_primers(self, *args, **kwargs):
fwd_gen = self.fwd.parse_primers(*args, **kwargs)
rev_gen = self.rev.parse_primers(*args, **kwargs)
generator = izip(fwd_gen, rev_gen)
return GenWithLength(generator, len(fwd_gen))
class PairedFASTA(object):
"""Read and write FASTA file pairs without using too much RAM"""
format = 'fasta'
def __len__(self): return self.count
def __iter__(self): return self.parse()
def __nonzero__(self): return bool(self.fwd) and bool(self.rev)
def __repr__(self): return '<%s object on "%s" and "%s">' % \
(self.__class__.__name__, self.fwd.path, self.rev.path)
def __enter__(self): return self.create()
def __exit__(self, exc_type, exc_value, traceback): self.close()
@property
def exists(self): return self.fwd.exists and self.rev.exists
def __init__(self, fwd, rev, parent=None):
# FASTA objects #
self.fwd = FASTA(fwd)
self.rev = FASTA(rev)
# Extra #
self.gzipped = self.fwd.gzipped
self.parent = parent
@property_cached
def count(self):
assert self.fwd.count == self.rev.count
return self.fwd.count
def open(self):
self.fwd.open()
self.rev.open()
def parse(self):
return izip(self.fwd.parse(), self.rev.parse())
def close(self):
self.fwd.close()
self.rev.close()
def create(self):
self.fwd.create()
self.rev.create()
return self
def add(self, f, r):
return self.add_pair((f,r))
def add_pair(self, pair):
self.fwd.add_seq(pair[0])
self.rev.add_seq(pair[1])
def remove(self):
self.fwd.remove()
self.rev.remove()
@property
def progress(self):
"""Just like self.parse but display a progress bar"""
return tqdm(self, total=len(self))
def subsample(self, down_to, dest_pair=None):
# Check size #
assert down_to < len(self)
# Make new pair of files #
if dest_pair is None:
dest_fwd_path = self.fwd_path.new_name_insert("subsampled")
dest_rev_path = self.rev_path.new_name_insert("subsampled")
dest_pair = self.__class__(dest_fwd_path, dest_rev_path)
# Do it #
dest_pair.create()
for pair in isubsample(self, down_to): dest_pair.add_pair(pair)
self.subsampled.close()
# Did it work #
assert len(dest_pair) == down_to
#------------------------------- Extensions ------------------------------#
def parse_primers(self, *args, **kwargs):
fwd_gen = self.fwd.parse_primers(*args, **kwargs)
rev_gen = self.rev.parse_primers(*args, **kwargs)
generator = izip(fwd_gen, rev_gen)
return GenWithLength(generator, len(fwd_gen))