INNER CODE UNIT · Python
run
sanger-pathogens/ariba · ariba/aln_to_metadata.py:248
def run(self, outprefix):
original_code = pyfastaq.sequences.genetic_code
pyfastaq.sequences.genetic_code = self.genetic_code
unpadded_seqs = AlnToMetadata._make_unpadded_seqs(self.padded_seqs)
insertions = AlnToMetadata._make_unpadded_insertion_coords(self.padded_seqs)
AlnToMetadata._check_sequences(self.padded_seqs, unpadded_seqs, self.refs_are_coding, genetic_code=self.genetic_code)
AlnToMetadata._variant_ids_are_unique(self.variants)
AlnToMetadata._check_variants_match_sequences(unpadded_seqs, self.variants, self.refs_are_coding, genetic_code=self.genetic_code)
tsv_lines = AlnToMetadata._variants_to_tsv_lines(self.variants, unpadded_seqs, self.padded_seqs, insertions, self.refs_are_coding, self.refs_are_variant_only)
with open(outprefix + '.tsv', 'w') as f:
print(*tsv_lines, sep='\n', file=f)
with open(outprefix + '.fa', 'w') as f:
for seqname in sorted(unpadded_seqs):
print(unpadded_seqs[seqname], sep='\n', file=f)
AlnToMetadata._make_cluster_file(unpadded_seqs, outprefix + '.cluster')