update changelog and bump version

Author: madeline-scyphers

CHANGELOG.md

@@ -2,6 +2,24 @@
 
 All notable changes to this project will be documented in this file.
 
+## 2.0.0-beta27 - 2026-03-18
+
+[f03804b](https://github.com/WrightonLabCSU/DRAM/commit/f03804bca43b15e55731316c00b1c34ac328c62c)...[7d9a12d](https://github.com/WrightonLabCSU/DRAM/commit/7d9a12d225c577a6b2fb0c4d7b1ba60a5588e1e8)
+
+### Features
+
+- Add a test version of dbcan3 to compare against dbcan2 ([efb3cc2](https://github.com/WrightonLabCSU/DRAM/commit/efb3cc23a5478f85e449099ec37285138cc5f8b7))
+
+  dbcan3 and dbcan3-sub test versions, will run both if run_dbcan3
+  option is present.
+
+- Switch hmmsearch to using PyHMMER search ([7d9a12d](https://github.com/WrightonLabCSU/DRAM/commit/7d9a12d225c577a6b2fb0c4d7b1ba60a5588e1e8))
+
+  PyHMMER has better parrallelism support, directly calling
+  the lower level C bindings for HMMER and rewriting how
+  it parallelizes. This means that when you had cpus=4 arg, it can
+  1/3 of the walltime with the exact same result.
+
 ## 2.0.0-beta26 - 2026-03-09
 
 [605d4f5](https://github.com/WrightonLabCSU/DRAM/commit/605d4f5d619d9f373352c8f400128066edcf58ef)...[91edea7](https://github.com/WrightonLabCSU/DRAM/commit/91edea7e6974be47da036f0f8af247d3d033326a)

bin/hmm_search.py

@@ -6,6 +6,7 @@
 
 alphabet = pyhmmer.easel.Alphabet.amino()
 
+
 @click.command()
 @click.option(
     "--hmm",
@@ -17,11 +18,7 @@
     type=click.Path(exists=True),
     help="Path to the input fasta to search against",
 )
-@click.option(
-    "--e_value",
-    type=float,
-    help="e value cutoff for filtering"
-)
+@click.option("--e_value", type=float, help="e value cutoff for filtering")
 @click.option(
     "--output_file",
     type=click.Path(),
@@ -43,15 +40,16 @@ def main(hmm, input_file, e_value, output_file, cpus):
     print(hmms)
 
     with open(output_file, "wb") as out_fh:
-
-        with pyhmmer.easel.SequenceFile(input_file, digital=True, alphabet=alphabet) as sf:
+        with pyhmmer.easel.SequenceFile(
+            input_file, digital=True, alphabet=alphabet
+        ) as sf:
             seqs = pyhmmer.easel.DigitalSequenceBlock(alphabet)
             seqs.extend(sf)
             first = True
             for hits in pyhmmer.hmmer.hmmsearch(hmms, seqs, cpus=cpus, E=e_value):
                 hits.write(out_fh, format="domains", header=first)
-                first=False
-            #total = sum(len(hits) for hits in pyhmmer.hmmer.hmmsearch(hmms, seqs, cpus=8, E=1e-15))
+                first = False
+            # total = sum(len(hits) for hits in pyhmmer.hmmer.hmmsearch(hmms, seqs, cpus=8, E=1e-15))
             print(f"pyhmmer search completed in {time.time() - t1:.3} seconds")
 
 

nextflow.config

@@ -481,7 +481,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=24'
-    version         = '2.0.0-beta26'
+    version         = '2.0.0-beta27'
     doi             = ''
 }