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Biotite 0.39.0

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@padix-key padix-key released this 05 Jan 17:04
v0.39.0
123e533
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Changelog

Additions

  • Add build for Python 3.12 (#513)
  • Added modern fast k-mer subsetting methods to sequence.align (#510)
    • These include:
      • MinimizerSelector
      • SyncmerSelector
      • CachedSyncmerSelector
      • MincodeSelector
    • The following k-mer ordering methods are available:
      • RandomPermutation
      • FrequencyPermutation
    • Added BucketKmerTable to support indexing of long k-mers with reasonable memory consumption
  • Support conversion of biotite.sequence.align.Alignment from/to CIGAR strings (#516)
    • read_alignment_from_cigar()
    • write_alignment_to_cigar()
  • Added sequence.graphics.plot_alignment_array() (#485)
  • Support new 5-character residue names in structures from PDB (#512)
  • Support NCBI API keys in database.entrez to increase download limits (#514)
  • Increased performance of application.sra(#504).
    • prefetch is called before fasterq_dump, as suggested here
    • FastaDumpApp is added, which decreases computation time by writing as FASTA instead of a FASTQ file, which omits the scores

Changes

  • application.sra.FastaDumpApp.get_sequences() now only returns sequence (#504) strings and not scores anymore (#504)
    • Use get_sequences_and_scores() instead

Fixes

  • Fixed memory leak in sequence.align.KmerTable.from_tables() (#510)
  • Fixed problems of plotting functionalities with recent Matplotlib versions (#518)
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