Read BLAST tab-separated output

read_blast(
  file,
  col_names = def_names("blast"),
  col_types = def_types("blast"),
  comment = "#",
  swap_query = FALSE,
  ...
)

Arguments

file

Either a path to a file, a connection, or literal data (either a single string or a raw vector).

Files ending in .gz, .bz2, .xz, or .zip will be automatically uncompressed. Files starting with http://, https://, ftp://, or ftps:// will be automatically downloaded. Remote gz files can also be automatically downloaded and decompressed.

Literal data is most useful for examples and tests. To be recognised as a path, it must be wrapped with I(), be a string containing at least one new line, or be a vector containing at least one string with a new line.

Using a value of clipboard() will read from the system clipboard.

col_names

column names to use. Defaults to def_names("blast") compatible with blast tabular output (--outfmt 6/7 in blast++ and -m8 in blast-legacy). def_names("blast") can easily be combined with extra columns: col_names = c(def_names("blast"), "more", "things").

col_types

column types to use. Defaults to def_types("gff3").

swap_query

if TRUE swap query and subject columns using swap_query() on import.