Read one or more BLAST tabular output files into ribbon_data format

`file` reads a single BLAST tabular output file; `files` reads multiple files at once and combines them. `files` accepts a character vector of literal paths and/or wildcard patterns (e.g. `"examples/blastn/*.o7"`).

Usage

read_blast(
  file = NULL,
  files = NULL,
  format = c("auto", "outfmt6", "outfmt7", "custom"),
  col_names = NULL,
  comment = "#",
  ...
)

Arguments

file

Optional path to a single BLAST tabular output file.

files

Optional character vector of BLAST tabular output files (literal paths and/or wildcard patterns). All matched files are read and combined into one data.frame.

format

Character. `"auto"` (default) detects the column layout from the number of columns; `"outfmt6"` / `"outfmt7"` require the standard 12/17-column layouts; `"custom"` requires `col_names`.

col_names

Optional character vector naming the columns in the file, used with `format = "custom"` or to override auto-detection.

comment

Character comment character, default `"#"` (BLAST outfmt 7 header lines start with `#`).

...

Additional arguments passed to [utils::read.table()] (e.g. `na.strings`).

Value

A data.frame with the required ribbon columns first (`qaccver`, `saccver`, `length`, `pident`, `qstart`, `qend`, `sstart`, `send`) followed by any preserved optional columns.

Examples

library(ggchord)
blast_file <- tempfile(fileext = ".o7")
writeLines(c(
  "# BLASTN 2.13.0+",
  "seqA  seqB  98.5  1200  18  0  1  1200  1  1200  1e-180  2400"
), blast_file)
read_blast(blast_file)
#>   qaccver saccver length pident qstart qend sstart send mismatch gapopen evalue
#> 1    seqA    seqB   1200   98.5      1 1200      1 1200       18       0 1e-180
#>   bitscore
#> 1     2400