read_blast {gggenomes}

Read BLAST tab-separated output

Description

Read BLAST tab-separated output

Usage

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 literal data, the input must be either 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() 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") (see def_types).

comment

character

swap_query

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

...

additional parameters, passed to read_tsv

Value

a tibble with the BLAST output