def __init__(self, HomologSet, alignment={}):
"""Object for maintaining alignment data for a HomologSet Object.
"""
self._HomologSet = HomologSet
self.Write = Write(self)
self.Read = Read(self)
self._alignments = {"latest": alignment}
def __init__(self, HomologSet, alignment={}):
"""Object for maintaining alignment data for a HomologSet Object.
"""
self._HomologSet = HomologSet
self.Write = Write(self)
self.Read = Read(self)
self._alignments = {"latest": alignment}
class Alignment(object):
def __init__(self, HomologSet, alignment={}):
"""Object for maintaining alignment data for a HomologSet Object.
"""
self._HomologSet = HomologSet
self.Write = Write(self)
self.Read = Read(self)
self._alignments = {"latest": alignment}
@property
def latest(self):
""" Return the latest alignment. """
return self._alignments["latest"]
@property
def n_taxa(self):
""" Return the number of sequences in alignment """
return len(self.latest)
@property
def length(self):
""" Return the length of the alignment. """
return len(list(self.latest.values())[0])
def list_alignments(self):
"""List the key for all alignments stored in this object."""
return list(self._alignments.keys())
def previous(self, key):
"""Get previous alignments
"""
return self._alignments[key]
def _move_old_alignment(self):
"""Moves the current alignment to new attribute name to make room for
a alignment.
"""
if self.latest != {}:
# Save old alignments.
exists = True
counter = 0
while exists == True:
if "align" + str(counter) in self._alignments:
counter += 1
else:
exists = False
# Move old alignment to new name.
self._alignments["align" + str(counter)] = self.latest
def add(self, alignment):
"""Add alignment data to object.
"""
self.Read._data_to_object(alignment)
def update(self, alignment_file):
""" Read in a manually edited alignment to Alignment object.
Reads in an alignment file and moves old alignments to new attribute.
"""
# Write out alignment file
self.Read.fasta(fname=alignment_file)
def subset(self, ids, alignment="latest"):
"""Return the a new Alignment object, which is a subset of full
class Alignment(object):
def __init__(self, HomologSet, alignment={}):
"""Object for maintaining alignment data for a HomologSet Object.
"""
self._HomologSet = HomologSet
self.Write = Write(self)
self.Read = Read(self)
self._alignments = {"latest": alignment}
@property
def latest(self):
""" Return the latest alignment. """
return self._alignments["latest"]
@property
def n_taxa(self):
""" Return the number of sequences in alignment """
return len(self.latest)
@property
def length(self):
""" Return the length of the alignment. """
return len(list(self.latest.values())[0])
def list_alignments(self):
"""List the key for all alignments stored in this object."""
return list(self._alignments.keys())
def previous(self, key):
"""Get previous alignments
"""
return self._alignments[key]
def _move_old_alignment(self):
"""Moves the current alignment to new attribute name to make room for
a alignment.
"""
if self.latest != {}:
# Save old alignments.
exists = True
counter = 0
while exists == True:
if "align" + str(counter) in self._alignments:
counter += 1
else:
exists = False
# Move old alignment to new name.
self._alignments["align" + str(counter)] = self.latest
def add(self, alignment):
"""Add alignment data to object.
"""
self.Read._data_to_object(alignment)
def update(self, alignment_file):
""" Read in a manually edited alignment to Alignment object.
Reads in an alignment file and moves old alignments to new attribute.
"""
# Write out alignment file
self.Read.fasta(fname=alignment_file)
def subset(self, ids, alignment="latest"):
"""Return the a new Alignment object, which is a subset of full
