bump PyHMMER version to 0.10.15

bakta/expert/protein_hmms.py

@@ -20,11 +20,10 @@ def search(cdss: Sequence[dict], user_hmms_path):
     proteins: list[pyhmmer.easel.DigitalSequence] = [ pyhmmer.easel.TextSequence(sequence=cds['aa'], name=bytes(orf.get_orf_key(cds), 'UTF-8')).digitize(alphabet) for cds in cdss ]
     with pyhmmer.plan7.HMMFile(user_hmms_path) as hmms_fh:
         hmms = list(hmms_fh)
-        hmms_id_desc = { hmm.accession.decode(): hmm.description.decode() for hmm in hmms }
         for hmm_query_hits in pyhmmer.hmmsearch(hmms, proteins, bit_cutoffs='trusted', cpus=cfg.threads):
-            hmm_id = hmm_query_hits.query_accession.decode()
-            hmm_length = hmm_query_hits.query_length
-            hmm_description = hmms_id_desc.get(hmm_id, '')
+            hmm_id = hmm_query_hits.query.accession.decode()
+            hmm_length = hmm_query_hits.query.M
+            hmm_description = hmm_query_hits.query.description.decode()
             hmms_description_fields = hmm_description.split('~~~')
             for hmm_query_hit in hmm_query_hits.reported:
                 aa_identifier = hmm_query_hit.name.decode()

environment.yml

@@ -14,7 +14,7 @@ dependencies:
   - aragorn>=1.2.41
   - infernal>=1.1.4
   - piler-cr
-  - pyhmmer>=0.10.14
+  - pyhmmer>=0.10.15
   - diamond==2.1.8
   - blast>=2.14.0
   - ncbi-amrfinderplus>=3.11.26

setup.py

@@ -32,7 +32,7 @@
         'alive-progress >= 3.0.1',
         'PyYAML >= 6.0',
         'pyrodigal >= 3.1.0',
-        'pyhmmer >= 0.10.14'
+        'pyhmmer >= 0.10.15'
     ],
     entry_points={
         'console_scripts': [