def alignment_to_partials(alignment, missing_data=None):
""" Generate a partials dictionary from a treeCl.Alignment """
partials_dict = {}
for (name, sequence) in alignment.get_sequences():
datatype = 'dna' if alignment.is_dna() else 'protein'
partials_dict[name] = seq_to_partials(sequence, datatype)
if missing_data is not None:
l = len(alignment)
for name in missing_data:
if name not in partials_dict:
partials_dict[name] = seq_to_partials('-'*l, datatype)
return partials_dict
def biopython_to_partials(alignment, datatype):
""" Generate a partials dictionary from a treeCl.Alignment """
partials_dict = {}
for seq in alignment:
partials_dict[seq.name] = seq_to_partials(seq, datatype)
return partials_dict