Comments (2)
current method
from pxblat import Client, Server
with Server() as server:
server.wait_for_ready()
client("atcg")
Future
from pxblat import Client, Server
with Server() as server:
server.wait_for_ready()
client(["atcg", "CTag"])
using gevent
as backend for multiple querys, and make multiple querys as default support.
from pxblat import Client, Server
with Server() as server:
server.wait_for_ready()
client(["atcg"])
Ideas
- support mixed usage of lower and upper case for sequences i.e. "atcg", "aTcg"
Performance Test
I did the performance evaluatation on the platform: OS: macOS 13.4.1 22F82 arm64 Host: MacBookPro18
.
The scripts locates on tests/test_result.py
Data Set | Samples | BLAT | PXBLAT(pool 1) | PXBLAT(pool 8) | PXBLAT(pool 4) |
---|---|---|---|---|---|
benchmark/fas/1 | 200 | 61.4011 | 50.4143 (1.2179x) | 50.4404 (1.2168x) | 50.6144 |
benchmark/fas/2 | 200 | 61.6994 | 51.0984 (1.2075x) | 51.7131 (1.1962x) | 50.9714 |
benchmark/fas/3 | 200 | 55.3351 | 46.4404 (1.1915x) | 46.5768 (1.1820x) | |
benchmark/fas/4 | 200 | 56.9760 | 47.7234 (1.1939x) | 47.2242 (1.1975x) | |
benchmark/fas/5 | 200 | 54.5457 | 46.4391 (1.1746x) | 45.4927 (1.1900x) |
from pxblat.
- https://pytest-benchmark.readthedocs.io/en/latest/usage.html
- https://github.com/bencherdev/bencher
- http://sdiehl.github.io/gevent-tutorial/
- https://www.gevent.org/api/gevent.greenlet.html#subclassing-greenlet
from pxblat.
Related Issues (18)
- Add contributor HOT 6
- Add twobit2fa binding and test it HOT 1
- Automate the workflow of verifying the result of pxblat is same as BLAT suit.
- Write document
- public to bioconda for x86 and aarch64 HOT 5
- fix the dug about serialize struct problem in macos
- Roadmap HOT 1
- Dependencies Errors in macos
- FIX: CI Error in macOS
- Client Limits: Too many open files HOT 1
- Add Docs
- Do not export `UsageStats`
- [Bug]: QueryResult is not a Bio object HOT 8
- I agree to follow this project's Code of Conduct
- [Bug]: Installation error on macos arm(M1/M2)
- [Bug]: Output is not a QueryResult HOT 15
- [Bug]: gfClient error exit HOT 11
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from pxblat.