R/linkBLAST.R

In palmid: RdRP Analysis Suite

# linkBLAST
#' Parse an input sequence into a BLAST-able HTML link
#'
#' @param header   character, header for blast search
#' @param aa.seq   character, query sequence (amino acid)
#' @param label    character, Display string["BLAST"]
#' @return character, html link for click to search
#' @keywords palmid sql BLAST html
#' @examples
#'
#' blast.link <- linkBLAST("u1337", "MYAASTRING", "BLAST")
#'
#' @import dplyr ggplot2
#' @export
linkBLAST <- function(header, aa.seq, label = "[BLAST]"){

  # Blast link preamble
  l0 <- "https://blast.ncbi.nlm.nih.gov/Blast.cgi"
  l1 <- "?PAGE_TYPE=BlastSearch&USER_FORMAT_DEFAULTS=on&SET_SAVED_SEARCH=true"
  l2 <- "&PAGE=Proteins&PROGRAM=blastp"
  l3q <- "&QUERY="
  l4t <- "&JOB_TITLE="
  l5 <- "&GAPCOSTS=11%201&DATABASE=nr&BLAST_PROGRAMS=blastp&MAX_NUM_SEQ=100&SHORT_QUERY_ADJUST=on&EXPECT=0.05"
  l6 <- "&WORD_SIZE=6&MATRIX_NAME=BLOSUM62&COMPOSITION_BASED_STATISTICS=2"
  l7 <- "&PROG_DEFAULTS=on&SHOW_OVERVIEW=on&SHOW_LINKOUT=on&ALIGNMENT_VIEW=Pairwise"
  l8 <- "&MASK_CHAR=2&MASK_COLOR=1&GET_SEQUENCE=on&NEW_VIEW=on"
  l9 <- "&NUM_OVERVIEW=100&DESCRIPTIONS=100&ALIGNMENTS=100&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML"

  # Construct link
  url.link <- paste0(
    "<a href='", l0, l1, l2,
    l3q, aa.seq,
    l4t, ">palmID_", header,
    l5, l6, l7, l8, l9,
    "' target='_blank'> ", label, "</a>"
  )

}