Current BUILD is being tested on linux and is not guaranteed to work on Windows. Binaries of older version available here
- GNU GCC >= 13.3.0
- CMake
- OpenMP support (-fopenmp)
- R > 4.4.0
- Rtools >= 4.4 (Windows)
sudo apt install libsqlite3-dev libeigen3-dev libboost-dev libfontconfig1-dev libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev cmake(Linux)
??QuickBLASTWritten in C++ and interfaced with R using Rcpp, the package is wrapped around ncbi-c++ toolkit's CBl2Seq Class (same with arrow) and exposing the functions to R with C linkage. I use getlogin() to store username in output metadata, this might raise red flags (in ArrowWrapper.cpp). QuickBLAST provides better interoperability with R for NCBI-BLAST. After much poking around, dependent libraries (Apache Arrow and NCBI-C++ Toolkit) are now compiled from scratch (and without Windows APIs on Windows - using MSYS2 and MinGW provided with RTools4.4).
The main difference between this PKG and the rest would be that + Quick blast is multi-threaded with { file reading (as chunks), BLASTing, wrapping hits into Arrow data structures }, and { writing of Arrow::RecordBatches to the output file in batches } is done in seperate threads. Hits are also converted into Rcpp::List if you want values to be returned to R. + QuickBLAST does not use Sys.Calls to invoke BLAST exes. You don't need BLAST programs in you system + BLAST DBs are not explicitly created
Cons : + Limited score attributes
Let me know if you want more information and please address bugs to me on github.
- Install Apache Arrow - (Optional).
- Install RTools 4.4 or greater - (For Windows. Rtools must be the same Major and Minor version of R)
devtools::install_github("https://github.com/vizkidd/QuickBLAST", force=T)List of available options can be checked with QuickBLAST::GetAvailableBLASTOptions() (Empty elements from the list are removed and BLAST defaults are set on the c++ side). Inputs and Outputs are provided as parameters and sequence specification(strand, sequence type) can be provided during QuickBLAST object creation with QuickBLAST::GetQuickBLASTInstance() (or use the QuickBLAST::BLAST*() functions in R). Enums used by QuickBLAST in C++ are not exposed in R and only integers are used, check QuickBLAST::GetQuickBLASTEnums().
?QuickBLAST::LoadBLASTHits- Implement more scores and filtering options
- Include function for reading the arrow output files
- Convert from arrow to GRanges (maybe with the use of arrow::Visit() functions)
Disclaimers for disclaimers, legal stuff for legal stuff and respect for respect, wherever it should go.