Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

fix getting the length of a generator #377

Merged
merged 3 commits into from
Jul 29, 2024
Merged

fix getting the length of a generator #377

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
9c5abd5
fix getting the length of a generator
rzlim08 Jul 26, 2024
890bbcb
copy generator to keep from destroying it
rzlim08 Jul 26, 2024
605e92a
fix linting
rzlim08 Jul 29, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
11 changes: 10 additions & 1 deletion lib/idseq_utils/idseq_utils/batch_run_helpers.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down Expand Up @@ -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,
Expand All @@ -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")):
Expand Down
Loading