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@github-actions github-actions released this 01 May 12:57
v0.6.0
04ccd31

Added

  • pyhmmer.daemon module with an client implementation to communicate to a hmmpgmd server.
  • Pipeline.arguments methods to get a list of CLI arguments from the parameters used to initialize the Pipeline.
  • Setters for name, accession and description properties of plan7.Hit.
  • Constructor for individual plan7.Trace objects outside a plan7.Traces list.
  • plan7.Trace.from_sequence constructor to create a faux trace from a single sequence.
  • manually_include and manually_drop methods to plan7.Hit for manually selecting the inclusion status of a Hit in a TopHits instance.
  • compare_ranking method to plan7.TopHits for comparing the order of the hits compared to a previous run on the same targets stored in an easel.KeyHash object.
  • Pipeline.iterate_seq and Pipeline.iterate_hmm to run iterative queries like JackHMMER.
  • repr implementations for easel.MSAFile, easel.SequenceFile and easel.HMMFile showing the path or file object they were created from.
  • repr implementation for easel.Randomness showing the seed and the RNG algorithm in use.
  • str implementation for plan7.Alignment using HMMER original code to display a domain alignment like in search/scan results.

Changed

  • plan7.Trace.posterior_probabilities property may now be None in case no memory is allocated for the posteriors in the P7_TRACE struct.
  • TopHits.to_msa can now add additional sequences passed as arguments to the alignment.
  • plan7.HMMPressedFile now raises an exception on attempts to create a new instance manually.
  • ignore_gaps argument of easel.SequenceFile is now deprecated.
  • repr implementations for easel types now use the fully qualified class name.

Fixed

  • easel.SequenceFile.readinto docstring not rendering properly in documentation.
  • Type annotations of hits_included and hits_reported of plan7.TopHits marking these properties as bool instead of int.
  • Setters of name, accession, description and author properties of easel.MSA crashing when given None values.
  • Exception value raised from Easel code not being properly extracted.
  • Plain strings being used in example for easel.TextSequence and easel.TextMSA constructors where byte strings are expected (#20).
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