INNER CODE UNIT · Python
alignment_filename
nickjcroucher/gubbins · python/gubbins/common.py:259
alignment_filename = base_filename + alignment_suffix
pre_process_snp_fasta = PreProcessFasta(snp_alignment_filename,
input_args.verbose,
0.0)
all_snp_alignment_length = pre_process_snp_fasta.get_alignment_length()
current_alignment_length = all_snp_alignment_length
os.symlink(os.path.join(current_directory,snp_alignment_filename),os.path.join(temp_working_dir,snp_alignment_filename))
else:
previous_tree_name = current_tree_name
alignment_filename = previous_tree_name + alignment_suffix
pre_process_snp_fasta = PreProcessFasta(alignment_filename,
input_args.verbose,
0.0)
if alignment_suffix.endswith('phylip'):
current_alignment_length = pre_process_snp_fasta.get_alignment_length('phylip-relaxed')
else:
current_alignment_length = pre_process_snp_fasta.get_alignment_length()