Current BUILD is being tested and is not guaranteed to work. Binaries of older version available here
- OpenMP support (-fopenmp)
- R > 4.4.1
- Rtools >= 4.4 (Windows)
??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)remotes::install_local("QuickBLAST_1.0_R_x86_64-pc-linux-gnu.tar.gz", build=F)
tblastx_ptr <- QuickBLAST::CreateNewBLASTInstance(seq_info = list(0,0,F), program = "tblastx", options = list("evalue"=1e-05, "pident"=0.75, "qcovhsp_perc"=0.75))
blastn_ptr <- QuickBLAST::CreateNewBLASTInstance(seq_info = list(0,0,F), program = "blastn", options = "")
QuickBLAST::BLAST2Files(ptr=tblastx_ptr, query="ungrouped.cds", subject="ungrouped.cds", out_file="out.tmp", seq_limit=1000, show_progress=T,return_values=F, num_threads=5)
QuickBLAST::BLAST2Seqs(ptr=tblastx_ptr, query="AAAAAAAAAAAAAAAAAAAAAAAAAAATTTTTTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGG", subject="TTTTTTTTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC")
QuickBLAST::BLAST2Seqs(ptr=blastn_ptr, query=">i11166\nTGGCACGTCTGGTAGCAGTTTGCAGGGAAGGGGAAGAGGAATACCCGTTTCTCGCCAGACAGATCC", subject=">i11167\nATGGCACGTCTGGTAGCAGTTTGCAGGGAAGGGGAAGAGGAATACCCGTTTCTCGCCAGACAGATCCCCCTCTTCATCGATGACACTCTCACGATGGTGATGGAGTTTTCCGATAGCGTCATGG")
QuickBLAST::BLAST1Folder(ptr = tblastx_ptr, input_folder="test", extension= ".cds", out_folder="test_out", num_threads=7, reciprocal_hits=F)
QuickBLAST::BLAST2Folders(ptr=blastn_ptr, query="query", subject="subject", extension = ".cds", out_folder="test2_out", num_threads=8, reciprocal_hits=F)
Same as BLAST but DB & OUTPUT Format are not available. 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().
- 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.