fix getting the length of a generator (#377)

* fix getting the length of a generator

* copy generator to keep from destroying it

* fix linting

lib/idseq_utils/idseq_utils/batch_run_helpers.py

@@ -13,6 +13,8 @@
 from typing import Dict, List, Optional
 from urllib.parse import urlparse
 
+from itertools import tee
+
 from idseq_utils.diamond_scatter import blastx_join
 from idseq_utils.minimap2_scatter import minimap2_merge
 
@@ -296,6 +298,12 @@ def _db_chunks(bucket: str, prefix):
             yield obj["Key"]
 
 
+def count_generator(gen):
+    gen, gen_copy = tee(gen)
+    generator_length = sum(1 for _ in gen_copy)
+    return generator_length, gen
+
+
 def run_alignment(
     input_dir: str,
     db_path: str,
@@ -321,7 +329,8 @@ def run_alignment(
         ]
         for chunk_id, db_chunk in enumerate(_db_chunks(db_bucket, db_prefix))
     )
-    with Pool(len(chunks)) as p:
+    chunk_length, chunks = count_generator(chunks)
+    with Pool(chunk_length) as p:
         p.starmap(_run_chunk, chunks)
     run(["s3parcp", "--recursive", chunk_dir, "chunks"], check=True)
     if os.path.exists(os.path.join("chunks", "cache")):