Commit d67573ac authored by Martin Larralde's avatar Martin Larralde
Browse files

Release v0.4.9

parent b435f9b1
Pipeline #26887 passed with stage
in 4 minutes and 55 seconds
......@@ -6,7 +6,26 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
## [Unreleased]
[Unreleased]: https://github.com/althonos/pyhmmer/compare/v0.4.8...HEAD
[Unreleased]: https://github.com/althonos/pyhmmer/compare/v0.4.9...HEAD
## [v0.4.9] - 2021-11-11
[v0.4.9]: https://github.com/althonos/pyhmmer/compare/v0.4.8...v0.4.9
### Added
- `plan7.ScoreData` class to store the substitution scores and maximal extensions for a long target search.
- `plan7.LongTargetsPipeline` to run searches on targets longer than 100,000 residues.
- `Alphabet` methods to check whether an `Alphabet` object is a DNA, RNA, nucleotide or protein alphabet.
- `window_length` and `window_beta` arguments to `plan7.Builder` to set the max length of nucleotide `HMM` created by builder objects.
### Changed
- `pyhmmer.hmmer.nhmmer` now uses a `LongTargetsPipeline` instead of a `Pipeline` to search the target sequences.
- `pyhmmer.hmmer.nhmmer` now supports `HMM` queries in addition to `DigitalSequence` and `DigitalMSA` queries.
- `pyhmmer.hmmer.phmmer` now always assumes protein queries.
- `Z` and `domZ` attributes of `plan7.TopHits` objects is now read-only.
### Fixed
- `nhmmer` now uses DNA as the default alphabet instead of amino acid alphabet like it did before ([#12](https://github.com/althonos/pyhmmer/issues/12)).
## [v0.4.8] - 2021-10-27
......
......@@ -25,7 +25,7 @@ from .hmmer import hmmalign, hmmsearch, hmmpress, nhmmer, phmmer
__author__ = "Martin Larralde <martin.larralde@embl.de>"
__license__ = "MIT"
__version__ = "0.4.8"
__version__ = "0.4.9"
__all__ = [
errors.__name__,
easel.__name__,
......
......@@ -3097,7 +3097,7 @@ cdef class Pipeline:
object incdomT=None,
str bit_cutoffs=None,
):
"""__init__(self, alphabet, background=None, *, bias_filter=True, null2=True, seed=42, Z=None, domZ=None, F1=0.02, F2=1e-3, F3=1e-5, E=10.0, T=None, domE=10.0, domT=None, incE=0.01, incT=None, incdomE=0.01, incdomT=None, bit_cutoffs=None, str strand=None)\n--
"""__init__(self, alphabet, background=None, *, bias_filter=True, null2=True, seed=42, Z=None, domZ=None, F1=0.02, F2=1e-3, F3=1e-5, E=10.0, T=None, domE=10.0, domT=None, incE=0.01, incT=None, incdomE=0.01, incdomT=None, bit_cutoffs=None)\n--
Instantiate and configure a new accelerated comparison pipeline.
......@@ -3689,7 +3689,7 @@ cdef class Pipeline:
.. versionadded:: 0.2.0
.. versionchanged:: 0.5.0
.. versionchanged:: 0.4.9
Query can now be a `Profile` or an `OptimizedProfile`.
"""
......@@ -4064,7 +4064,7 @@ cdef class Pipeline:
cdef class LongTargetsPipeline(Pipeline):
"""An HMMER3 pipeline tuned for long targets.
.. versionadded:: 0.5.0
.. versionadded:: 0.4.9
"""
......@@ -4082,10 +4082,10 @@ cdef class LongTargetsPipeline(Pipeline):
int B1=100,
int B2=240,
int B3=1000,
int block_length=1024*256,
int block_length=0x40000,
**kwargs,
):
"""__init__(self, alphabet, background=None, *, bias_filter=True, null2=True, seed=42, Z=None, domZ=None, F1=0.02, F2=1e-3, F3=1e-5, E=10.0, T=None, domE=10.0, domT=None, incE=0.01, incT=None, incdomE=0.01, incdomT=None, bit_cutoffs=None, str strand=None)\n--
"""__init__(self, alphabet, background=None, *, F1=0.02, F2=3e-3, F3=3e-5, strand=None, B1=100, B2=240, B3=1000, block_length=0x40000, **kwargs)\n--
Instantiate and configure a new long targets pipeline.
......@@ -4120,7 +4120,7 @@ cdef class LongTargetsPipeline(Pipeline):
if not alphabet.is_nucleotide():
raise ValueError(f"Expected nucleotide alphabet, found {alphabet!r}")
# create the pipeline
super().__init__(alphabet, background, **kwargs)
super().__init__(alphabet, background, F1=F1, F2=F2, F3=F3, **kwargs)
# set the options for long targets
self._pli.long_targets = True
self._pli.block_length = block_length
......
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