althonos/pyhmmer: v0.6.1

Published June 28, 2022 | Version v0.6.1

Software Open

Added

pickle protocol support for TopHits objects, using the HMMER network serialization.
TopHits.write method to write hits to a file in tabular format.
query_name and query_accession properties to TopHits objects to access the name and accession of the query that produced the hits.

Fixed

Extraction of filename from file-like objects in the HMMFile constructor.
Use os.cpu_count instead of multiprocessing.cpu_count where applicable to preserve OS scheduling.
Wrong return type in docstring of HMM.insert_emissions.
TopHits.searched_nodes returning the searched number of residues instead of the searched number of model nodes.
Unsound decoding of pickled MatrixF or VectorF when data comes from a source of different endianness.

Changed

Rewrite pyhmmer.hmmer threading code using Deque instead of collections.Queue to store the queries and results.
Reduce memory consumption of pyhmmer.hmmer by reducing the number of semaphores and event flags used concurrently.
Make pyhmmer.hmmer main threads block on query insertion rather than result retrieval to make sure worker threads are never idling.

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althonos/pyhmmer-v0.6.1.zip md5:bf72af48371676eed2b7e1cc57aa6a93	8.8 MB	Preview Download