Read and parse BUSCO's summary report — read_busco • cogeqc

Read and parse BUSCO's summary report

Usage

read_busco(result_dir = NULL)

Arguments

result_dir: Path to the directory where BUSCO results are stored. This function will look for the short_summary* file (single run) or short_summary* file (batch mode).

Value

A data frame with the following variables:

Class: BUSCO class. One of Complete_SC, Complete_duplicate, Fragmented, or Missing
Frequency: Frequency of BUSCOs in each class. If BUSCO was run in batch mode, this variable will contain relative frequencies. If BUSCO was run for a single file, it will contain absolute frequencies.
Lineage: Name of the lineage dataset used.
File (batch mode only): Name of the input FASTA file.

Examples

result_dir <- system.file("extdata", package = "cogeqc")
df <- read_busco(result_dir)