INNER CODE UNIT · Python
get_alignment_information
nickjcroucher/gubbins · python/gubbins/PreProcessFasta.py:120
def get_alignment_information(self, format = "fasta"):
sequence_names = []
base_frequencies = [0,0,0,0]
alignment = AlignIO.read(self.input_filename, format)
alignment_length = alignment.get_alignment_length()
for record in alignment:
sequence_names.append(record.id)
for index,base in enumerate(['A','C','G','T']):
base_frequencies[index] += (record.seq.count(base) + record.seq.count(base.lower()))
base_frequencies = [b/(alignment_length*len(sequence_names)) for b in base_frequencies]
return alignment_length, sequence_names, base_frequencies