read_blast: Read a BLAST .tsv files

In thackl/thacklr: A Collection of R Functions and Snippets I Often Use.

Read a BLAST .tsv files

Description

Read a BLAST output in '-outfmt 6/7' format (o6/o7). If BLAST was run with custom column specifiers, those have to be passed to the call.

Usage

read_blast(file, col_spec = "std")

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_spec

BLAST custom column specifiers

Details

Uses "# " to identify and ignore comment lines in o7. NOTE that any line containing this string anywhere, not limited to the line start will be trimmed after the "# ".

Value

tibble

thackl/thacklr documentation built on Oct. 16, 2023, 9:15 p.m.