phylotypr 0.2.0

New features

• Add new function classify_sequences(), which has confidence score filtering built-in as an option and is multithreaded by default. Can be run by giving the function the name of a data frame and the columns corresponding to the sequence id and sequences or as a {strollur} object and function will be output results as appropriate

Improvements

• Update vignettes and documentation for new functions and features
• Core functions can now process more than one sequence at a time
• Added type checking and check for column names in classify_sequences(), filter_taxonomy(), print_taxonomy()
• build_kmer_database() now includes reference_data argument
• modified filter_taxonomy() to take a data frame rather than a list
• modified print_taxonomy() to take a data frame rather than a list and then output mothur-like taxonomy string to user specified depth. If specified depth is shorter than observed, string gets truncated. If depth is longer than specified it adds “_unclassified”. User can turn off confidence scores
• rdp_trainset9_pds and rdp_trainset9 now include reference data as a data frame in the reference_data slot; will be incorporated in databases provided by {phylotyprrefdata}. These were renamed from trainset9_rdp and trainset9_pds
• Changed id to sequence_name across functions
• Modify read_fasta to convert non-ATGCU-. to N; force capitalization. This was also applied to built in reference data
• Remove use of set.seed() to be within call to classify_sequences()
• Optimized build_kmer_database() and classify_sequences() for performance making both significantly faster

Deprecated functions

• classify_sequence()

Bug fixes

• Nothing to repair - if you find something let us know!

phylotypr 0.1.1

This is a patch release to… * update the citation * change the license to GPL v3 * make a small change to the behavior of the code for when a k-mer shows up more than once in a sequence

phylotypr 0.1.0

This is the first release version of phylotypr! 🎉

• Functions:
  • read_fasta()
  • read_taxonomy()
  • build_kmer_database()
  • classify_sequence()
  • filter_taxonomy()
  • print_taxonomy()
• Example datasets:
  • trainset9_rdp
  • trainset9_pds
• Vignette:
  • Getting started