read_context: Read files in different contexts

In thackl/gggenomes: A Grammar of Graphics for Comparative Genomics

Read files in different contexts

Description

Powers read_seqs(), read_feats(), read_links()

Usage

read_context(
  files,
  context,
  .id = "file_id",
  format = NULL,
  parser = NULL,
  ...
)

Arguments

files	files to reads. Should all be of same format. In many cases, compressed files (.gz, .bz2, .xz, or .zip) are supported. Similarly, automatic download of remote files starting with ⁠http(s)://⁠ or ⁠ftp(s)://⁠ works in most cases.
context	the context ("seqs", "feats", "links") in which a given format should be read.
.id	the column with the name of the file a record was read from. Defaults to "file_id". Set to "bin_id" if every file represents a different bin.
format	specify a format known to gggenomes, such as gff3, gbk, ... to overwrite automatic determination based on the file extension (see def_formats() for full list).
parser	specify the name of an R function to overwrite automatic determination based on format, e.g. parser="read_tsv".
...	additional arguments passed on to the format-specific read function called down the line.

Functions

• read_context(): bla keywords internal

thackl/gggenomes documentation built on March 10, 2024, 7:26 a.m.