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biohansel v2.6.0

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@peterk87 peterk87 released this 05 Mar 03:35
· 4 commits to master since this release
e7f5b14

Changes

  • Added min kmer fraction threshold (#140)
    • added --min-kmer-frac for exclusion of low abundance kmers from subtype calling
    • detailed report adds columns: kmer_fraction, total_refposition_kmer_frequency, is_kmer_fraction_okay
    • increased default --max-kmer-freq for amplicon seq data compatibility
  • Added bump2version config for easy version updating (#141)
    • Bump version with $ bump2version major|minor|patch
  • Codebase clean-up (#143)
    • Added Rich for logging and informative tracebacks
    • refactoring and reformatting; fixed some docstrings; simplified some logic
    • moved some functions to more appropriate places
    • replaced string.format with f-string literals
    • moved check_total_kmers call to right after parsing of CLI args
    • replaced bio_hansel.parsers._parse_fasta with BioPython's Bio.SeqIO.FastaIO.SimpleFastaParser; forcing uppercase of sequence
    • cleaned up some tests
    • updated help message to show program name and version as well as nice list of built-in schemes
    • ignoring/fixed some warnings when pytest