Commits · 02270aa4fb748797defdd3554c77a84dfa4ee3d6 · Martin Larralde / pyhmmer · GitLab

27 Jun, 2022 1 commit
- Implement `__getstate__` for `Alignment` and `Domain` classes · 02270aa4
  Martin Larralde authored Jun 27, 2022
  
  02270aa4
01 May, 2022 1 commit
- Add `__repr__` implementation to `pyhmmer.plan7.HMMFile` · 27bc3570
  Martin Larralde authored May 01, 2022
  
  27bc3570
27 Apr, 2022 1 commit
- Fix methods used for manually controlling the inclusion of a `Hit` · e19d427e
  Martin Larralde authored Apr 27, 2022
  
  e19d427e
23 Apr, 2022 4 commits
- Fix type annotations of `TopHits.hits_included` and `TopHits.hits_reported` · 9150a6e4
  Martin Larralde authored Apr 23, 2022
  
  9150a6e4
- Rename `SearchIteration` to `IterationResult` for consistency · bcbecab5
  Martin Larralde authored Apr 23, 2022
  
  bcbecab5
- Add custom class to run iterative search queries against a HMMER daemon · 317e1bd3
  Martin Larralde authored Apr 23, 2022
  
  317e1bd3
- Add `select_hits` argument to iterative search methods of `Pipeline` · df08b4d7
  Martin Larralde authored Apr 23, 2022
  
  df08b4d7
22 Apr, 2022 4 commits
- Fix minor issues in the documentation of `pyhmmer.daemon` and the type... · 3839800d
  Martin Larralde authored Apr 22, 2022
```
Fix minor issues in the documentation of `pyhmmer.daemon` and the type annotations of `pyhmmer.plan7`
```
  3839800d
- Use a Cython namedtuple-style class for results in each `IterativeSearch` iteration · fd3bbf91
  Martin Larralde authored Apr 22, 2022
  
  fd3bbf91
- Add `Pipeline.iterate_seq` to run `jackhmmer`-style homology searches · 5b58f0e6
  Martin Larralde authored Apr 22, 2022
  
  5b58f0e6
- Add the `TopHits.compare_ranking` method to compare ranked hits to a previous run · 8289b4bc
  Martin Larralde authored Apr 22, 2022
  
  8289b4bc
21 Apr, 2022 4 commits
- Update `TopHits.to_msa` to support adding additional sequences to the alignment · 9b5e98d0
  Martin Larralde authored Apr 21, 2022
  
  9b5e98d0
- Add a constructor for individual `Trace` objects · 88e352c9
  Martin Larralde authored Apr 21, 2022
  
  88e352c9
- Make `plan7.Trace.posterior_probabilities` optional in case memory is not allocated · 3b7e123b
  Martin Larralde authored Apr 21, 2022
  
  3b7e123b
- Add setters for `Hit.name`, `Hit.accession` and `Hit.description` properties · b6858399
  Martin Larralde authored Apr 21, 2022
  
  b6858399
20 Apr, 2022 1 commit
- Add type stubs for `pyhmmer.daemon` and fix remaining `mypy` errors · 6e716e33
  Martin Larralde authored Apr 20, 2022
  
  6e716e33
19 Apr, 2022 1 commit
- Add `Pipeline.arguments` method to show a pipeline configuration as CLI flags · a4eff443
  Martin Larralde authored Apr 19, 2022
  
  a4eff443
01 Mar, 2022 4 commits
- Update `TopHits.merge` to support more than one argument · d73c0d70
  Martin Larralde authored Mar 01, 2022
  
  d73c0d70
- Update management of pipeline parameters in `TopHits` code · 86909db4
  Martin Larralde authored Mar 01, 2022
  
  86909db4
- Implement `TopHits.merge` to merge two collections of hits · 434b0c6a
  Martin Larralde authored Mar 01, 2022
  
  434b0c6a
- Implement `TopHits.copy` by manually copying all hits and domains · af5ec9a0
  Martin Larralde authored Mar 01, 2022
  
  af5ec9a0
24 Dec, 2021 3 commits
- Fix some type issues in `pyhmmer.plan7` and `pyhmmer.hmmer` · 928c1164
  Martin Larralde authored Dec 24, 2021
  
  928c1164
- Update `pyhmmer.hmmer` to use the `PipelineSearchTargets` collection when possible · fa110a5b
  Martin Larralde authored Dec 24, 2021
  
  fa110a5b
- Add a dedicated collection to store the target sequences of a `Pipeline` · 27d9d8a1
  Martin Larralde authored Dec 24, 2021
  
  27d9d8a1
14 Dec, 2021 6 commits
- Implement `__sizeof__` for `Profile` and `OptimizedProfile` in `plan7` · 69346f85
  Martin Larralde authored Dec 15, 2021
  
  69346f85
- Add `OptimizedProfile.__eq__` implementation using `p7_oprofile_Compare` · bf4d0762
  Martin Larralde authored Dec 15, 2021
  
  bf4d0762
- Add some missing getters for `OptimizedProfile` attributes · d31ea8fc
  Martin Larralde authored Dec 14, 2021
  
  d31ea8fc
- Add method to read the optimized profiles from a pressed HMM file · e4f680f4
  Martin Larralde authored Dec 14, 2021
  
  e4f680f4
- Add `HMMFile.is_pressed` method and `HMMFile.closed` property to `plan7.pyx` · 869ce907
  Martin Larralde authored Dec 14, 2021
  
  869ce907
- Add `HMMFile.read` method to read a single HMM from the file · 022e6ae1
  Martin Larralde authored Dec 14, 2021
  
  022e6ae1
05 Dec, 2021 4 commits
- Add method to compute the match state occupancy of a `plan7` HMM model · 0ccc364c
  Martin Larralde authored Dec 05, 2021
  
  0ccc364c
- Allow setting a different score matrix in `Builder` constructor · b78d70d1
  Martin Larralde authored Dec 05, 2021
  
  b78d70d1
- Add several methods to `plan7.HMM` to compute model statistics · fbf3ea0b
  Martin Larralde authored Dec 05, 2021
  
  fbf3ea0b
- Fix `Builder` always using gap probabilities even when building HMMs from an MSA · cfa68aee
  Martin Larralde authored Dec 03, 2021
  
  cfa68aee
11 Nov, 2021 3 commits
- Use module-level constant tables to translate strings to enums in `plan7` and `easel` · b435f9b1
  Martin Larralde authored Nov 11, 2021
  
  b435f9b1
- Revert back to creating `Offset`, `Cutoffs` and `EvalueParameters` lazily · ec4fb0d7
  Martin Larralde authored Nov 11, 2021
  
  ec4fb0d7
- Make `Pipeline.search_hmm` accept a `Profile` or `OptimizedProfile` directly · 57673d74
  Martin Larralde authored Nov 11, 2021
  
  57673d74
10 Nov, 2021 1 commit
- Add dedicated `Pipeline` subclass for long targets searches · 7cc51d46
  Martin Larralde authored Nov 10, 2021
  
  7cc51d46
01 Nov, 2021 2 commits
- Add `strand` keyword argument to configure a `Pipeline` for nucleotide sequences · c8c770da
  Martin Larralde authored Nov 01, 2021
  
  c8c770da
- Add the `plan7.ScoreData` structure required for long target searches · 7dc0b922
  Martin Larralde authored Nov 01, 2021
  
  7dc0b922