read_fai: Read fasta index

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

Read fasta index

Description

Read seq_ids and lengths from a samtools/seqkit faidx file or from a fasta directly (requires seqkit in path). Seqkit is preferred because it allows reading the full header including seq description.

Usage

read_fai(
  file,
  col_names = c("seq_id", "seq_desc", "length"),
  keep_index = FALSE
)

Arguments

file	.fai/.seqkit.fai (plain/pipe), .fa (plain)
col_names	custom column names
keep_index	do not ignore index columns with length offsets etc.

Details

Note, only .fai connections can be pipes, .fa have to be plain text files.

Value

tibble

Examples

read_fai("foo.fa.fai")  # samtools style index, no description
read_fai("foo.fa.seqkit.fai") # seqkit style with description
# custom col_names and keep index info
read_fai("foo.fa.fai", keep_index=T, col_names=c("contig_id", "contig_desc", "len"))

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