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pyhmmer

0.12.3althonos/pyhmmer ↗New releases in your daily digest, changelog included.

Cython bindings and Python interface to HMMER3.

Release timeline

68 releases since 2020

2020202120222023202420252026

20202026

One column per quarter.

pyhmmer.plan7.Builder class to handle building a HMM from a sequence.
Pipeline.search_seq to query a sequence against a sequence database.
psutil dependency to detect the most efficient thread count for hmmsearch based on the number of physical CPUs.
pyhmmer.hmmer.phmmer function to run a search of query sequences against a sequence database.

Inaccurate exception messages in Pipeline.search_hmm.
Unneeded RNG reallocation, replaced with re-initialisation where possible.
SequenceFile.__next__ not working after being set in digital mode.
sequences argument of hmmsearch now only requires a typing.Collection[DigitalSequence] instead of a typing.Collection[Sequence] (not more __getitem__ needed).

hits argument to Pipeline.search_hmm to reduce risk of issues with TopHits reuse.
Broken alignment coordinates on Domain classes.

0.1.415 Jan 20213 sources agree

[v0.1.4]: https://github.com/althonos/pyhmmer/compare/v0.1.3...v0.1.4

DigitalSequence.textize to convert a digital sequence to a text sequence.
DigitalSequence.__init__ method allowing to create a digital sequence from any object implementing the buffer protocol.
Alignment.hmm_accession property to retrieve the accession of the HMM in an alignment.

0.1.12 Dec 20203 sources agree

[v0.1.1]: https://github.com/althonos/pyhmmer/compare/v0.1.0...v0.1.1

HMMFile calling file.peek without arguments, causing it to crash when passed some types, e.g. gzip.GzipFile.
HMMFile failing to work with PyPy file objects because of a bug with their implementation of readinto.
C/Python file object implementation using strcpy instead of memcpy, causing issues when null bytes were read.

0.1.01 Dec 20203 sources agree

[v0.1.0]: https://github.com/althonos/pyhmmer/compare/v0.1.0-a5...v0.1.0

Initial beta release.