tr_anno_cleaner: Clean annotations from pseudomonas.com

In travis-m-blimkie/tRavis: tRavis: an R package by Travis Blimkie

Clean annotations from pseudomonas.com

Description

Given an input CSV or TSV annotation file from https://pseudomonas.com, separates and cleans the data, returning a tidy tibble with the following columns: "locus_tag", "gene_name", and "product_name". Setting the extra_cols argument to TRUE will add the columns "start", "end", and "strand". Enabling fill_names will populate missing gene names with the corresponding locus tag.

Usage

tr_anno_cleaner(input_file, extra_cols = FALSE, fill_names = FALSE)

Arguments

input_file	Path to the input TSV or CSV file.
extra_cols	Logical to determine if start, end, and strand columns should be included. Defaults to FALSE.
fill_names	Logical to determine if blank/NA genes names should be filled in with corresponding locus tag. Defaults to FALSE.

Value

A data frame (tibble) of the cleaned input file

References

Download annotation files from https://pseudomonas.com

See Also

https://www.github.com/travis-m-blimkie/tRavis

Examples

tr_anno_cleaner(
  input_file = paste0(
  "https://pseudomonas.com/downloads/pseudomonas/pgd_r_22_1/",
  "Pseudomonas_aeruginosa_PAO1_107/Pseudomonas_aeruginosa_PAO1_107.csv.gz"
  )
)

travis-m-blimkie/tRavis documentation built on April 9, 2024, 11:45 p.m.