NEWS

phylotypr 0.2.0

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

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

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

This is the first release version of phylotypr! 🎉