Commit 684a54a7 authored by Martin Larralde's avatar Martin Larralde
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Release v0.3.0

parent 8104fc16
Pipeline #20732 passed with stage
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......@@ -6,7 +6,40 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
## [Unreleased]
[Unreleased]: https://github.com/althonos/pyhmmer/compare/v0.2.2...HEAD
[Unreleased]: https://github.com/althonos/pyhmmer/compare/v0.3.0...HEAD
## [v0.3.0] - 2021-03-11
[v0.3.0]: https://github.com/althonos/pyhmmer/compare/v0.2.2...v0.3.0
## Added
- `easel.MSAFile` to read from a file containing
- `accession`, `author`, `name` and `description` properties to `easel.MSA` objects.
- `plan7.Builder.build_msa` to build a pHMM from a sequence alignment.
- Additional methods to `easel.KeyHash`, allowing to use it as a `dict`/`set` hybrid.
- `Sequence.write` and `MSA.write` methods to format a sequence or an alignment to a file handle.
- `plan7.TopHist.to_msa` method to convert all the top hits of a query against a database into a multiple sequence alignment.
- `easel.MSA.sequences` attribute to access individual sequences of an alignment using the `collections.abc.Sequence` interface.
- `easel.DigitalMSA.textize` method to convert a multiple sequence alignment in digital mode to its text-mode counterpart.
- Read-only `name`, `accession` and `description` properties to `plan7.Profile` showing attributes inherited from the HMM it was configured with.
- `plan7.HMM.consensus` property, allowing to access the consensus sequence of a pHMM.
- `plan7.HMM` equality implementation, using zero tolerance.
- `plan7.Pipeline.search_msa` to query a MSA against a sequence database.
- `easel.Sequence.reverse_complement` method allowing to reverse-complement inplace or to build a copy.
- `errors.AlphabetMismatch` exception for use in cases where an alphabet is expected but not matched by the input.
- `hmmer.nhmmer` function with the same behaviour as `hmmer.phmmer`, except it expects inputs with a DNA alphabet.
### Fixed
- `plan7.Builder.copy` not copying some parameters correctly, causing `pyhmmer.hmmer.phmmer` to give inconsistent results in multithreaded mode.
- `easel.Bitfield` not properly handling index overflows.
- Documentation not rendering for the `__init__` method of all classes.
### Changed
- `plan7.Builder` gap-open and gap-extend probabilities are now set on instantiation and depend on the alphabet type.
- Constructors for `easel.TextMSA` and `easel.DigitalMSA`, which can now be given an iterable of `easel.Sequence` objects to store in the alignment.
### Removed
- Unimplemented `easel.SequenceFile.fetch` and `easel.SequenceFile.fetchinto` methods.
## [v0.2.2] - 2021-03-04
......
......@@ -25,7 +25,7 @@ from .hmmer import hmmsearch, hmmpress, phmmer
__author__ = "Martin Larralde <martin.larralde@embl.de>"
__license__ = "MIT"
__version__ = "0.2.2"
__version__ = "0.3.0"
__all__ = [
errors.__name__,
easel.__name__,
......
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