def parse_input(target_sequence: str, input_fasta_file: str) -> None:
"""
parse_input
:param target_sequence: The target sequence as a string.
:param input_fasta_file: The path to a FASTA file.
"""
if not Helpers.valid_dna_sequence(target_sequence):
raise click.UsageError(
'The target sequence is not a valid DNA sequence.')
input_sequence = Helpers.fasta_file_to_sequence(input_fasta_file)
if not input_sequence:
raise click.UsageError('Passed input file not in FASTA format.')
optimal_alignment_finder = OptimalAlignmentFinder(target_sequence,
input_sequence)
# If the results directory doesn't exist, create it.
if not os.path.exists(RESULTS_DIRECTORY):
os.makedirs(RESULTS_DIRECTORY)
Alignment.save_alignments(f'{RESULTS_DIRECTORY}forward_alignments.json',
optimal_alignment_finder.forward_alignments)
Histogram.save_histograms(optimal_alignment_finder.forward_alignments,
True)
Alignment.save_alignments(
f'{RESULTS_DIRECTORY}reverse_complement_alignments.json',
optimal_alignment_finder.reverse_complement_alignments)
Histogram.save_histograms(
optimal_alignment_finder.reverse_complement_alignments, False)