dot_blast: Wrapper for the new NCBI BLAST+ tools

In gschofl/blastr: A wrapper for NCBI Blast

Description

Wrapper for the new NCBI BLAST+ tools

Usage

.blast(exec, query, db, outfmt = "xml", max_hits = 20, strand = "both",
  ..., intern = FALSE, show_cmd = FALSE, parse = TRUE)

Arguments

query	Query sequences as path to a FASTA file, an XStringSet object, or a character vector.
db	Blast database name (defaults to 'nt' for blastn and 'nr' for the rest).
outfmt	XML or table (default: XML)
max_hits	Maximum number of hits to return. (defaults: 20) Sets the '-max_target_seqs' parameter internally.
strand	Query strand(s) to seach against database.
...	Arguments passed on to the blast commmand line tools.
intern	Set TRUE if no '-out' argument is specified. Captures the blast output in an R character vector.
show_cmd	If TRUE print the constructed command line instead of passing it to system.
parse
program	One of blastn, blastp, blastx, tblastn, or tblastx

gschofl/blastr documentation built on May 17, 2019, 8:52 a.m.