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)