Update Pyrodigal to 3.0.0

RasmussenLab · Sep 18, 2023 · c543d36 · c543d36
1 parent 1c511a9
commit c543d36
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -6,7 +6,7 @@ dependencies = [
     "torch == 1.13.1",
     "pycoverm == 0.6.0",
     "pyhmmer == 0.10.2",
-    "pyrodigal == 2.3.0"
+    "pyrodigal == 3.0.0"
 ]
 # Currently pycoverm does not have binaries for Python > 3.11.
 # The dependency resolver, will not error on Python 3.11, but attempt

diff --git a/vamb/parsemarkers.py b/vamb/parsemarkers.py
@@ -242,7 +242,7 @@ def process_chunk(
     chunk: list[FastaEntry],
     hmms: list[pyhmmer.plan7.HMM],
     name_to_id: dict[MarkerName, MarkerID],
-    finder: pyrodigal.OrfFinder,
+    finder: pyrodigal.GeneFinder,
 ) -> list[tuple[ContigID, np.ndarray]]:
     # We temporarily store them as sets in order to deduplicate. While single contigs
     # may have duplicate markers, it makes no sense to count this as contamination,
@@ -288,7 +288,7 @@ def work_per_process(
     # allowing pyhmmer to scan multiple sequences at once for speed
     chunk: list[FastaEntry] = []
     result: list[tuple[ContigID, np.ndarray]] = []
-    finder = pyrodigal.OrfFinder(meta=True)
+    finder = pyrodigal.GeneFinder(meta=True)
     with open(contig_path, "rb") as file:
         for record in byte_iterfasta(file):
             chunk.append(record)