adjust ranks of user-provided proteins and HMMs

Increase the rank of user-provided proteins to 101, so that they have higher ranks than user-provided HMMs, which in turn are ranked 100, thus higher than all non-user-provided annotation sources.
oschwengers · Sep 24, 2024 · c7046ab · c7046ab
1 parent 091d0b0
commit c7046ab
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/bakta/expert/protein_hmms.py b/bakta/expert/protein_hmms.py
@@ -58,7 +58,7 @@ def search(cdss: Sequence[dict], user_hmms):
                     hit = {
                         'type': 'user_hmms',
                         'source': 'UserHMMs',
-                        'rank': 99,
+                        'rank': 100,
                         'id': hmm_id,
                         'length': hit_domain_lengths_sum,
                         'aa_cov': aa_cov,

diff --git a/bakta/expert/protein_sequences.py b/bakta/expert/protein_sequences.py
@@ -117,7 +117,7 @@ def write_user_protein_sequences(aa_fasta_path: Path):
             with aa_fasta_path.open('w') as fh_out:
                 for user_protein in user_proteins:
                     (model_id, min_id, min_query_cov, min_model_cov, gene, product, dbxrefs, seq) = user_protein
-                    fh_out.write(f">{model_id} UserProteins~~~{100}~~~{min_id}~~~{min_query_cov}~~~{min_model_cov}~~~{gene}~~~{product}~~~{','.join(dbxrefs)}\n{seq}\n")
+                    fh_out.write(f">{model_id} UserProteins~~~{101}~~~{min_id}~~~{min_query_cov}~~~{min_model_cov}~~~{gene}~~~{product}~~~{','.join(dbxrefs)}\n{seq}\n")
                     log.debug(
                         'imported user aa: id=%s, length=%i, min-id=%f, min-query-cov=%f, min-model-cov=%f, gene=%s, product=%s, dbxrefs=%s',
                         model_id, len(seq), min_id, min_query_cov, min_model_cov, gene, product, dbxrefs