def align(self, degappify=False):
"""align(degappify=False) : Align all EntryGroups in a multiple sequence alignment, using the master entries.
If degappify==True, will first remove all gaps from sequences before realigning.
Calls gappify() on all EntryGroups after performing the alignment.
"""
from prosci.util.seq import align as seqalign
if degappify:
self.remove_gaps()
aligned = Ali(seqalign(self.toFastaString()), fasta_mode=True)
for eg_self, eg_aligned in zip(self, aligned):
assert deGappify(eg_aligned.master.seq) == deGappify(eg_self.master.seq)
eg_self.master.seq = eg_aligned.master.seq
eg_self.gappify()
def align(self, other, degappify=False):
"""align(other, degappify=False) : Align this Entry to another using a sequence alignment.
If degappify==True, will first remove all gaps from sequences before realigning.
"""
from prosci.util.seq import align as seqalign
assert self.code != other.code
if degappify:
self.seq = deGappify(self.seq)
other.seq = deGappify(other.seq)
aligned = Ali(seqalign(self.toFastaString()+other.toFastaString()), fasta_mode=True)
assert len(aligned) == 2
assert deGappify(aligned[self.code].master.seq) == deGappify(self.seq)
assert deGappify(aligned[other.code].master.seq) == deGappify(other.seq)
self.seq = aligned[self.code].master.seq
other.seq = aligned[other.code].master.seq