Clean annotations from pseudomonas.com

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

link <- system.file(
  "extdata/Pseudomonas_aeruginosa_PAO1_107.csv.gz",
  package = "tRavis"
)

tr_anno_cleaner(input_file = link)
#> # A tibble: 5,713 × 3
#>    locus_tag gene_name product_name                                  
#>    <chr>     <chr>     <chr>                                         
#>  1 PA0001    dnaA      chromosomal replication initiator protein DnaA
#>  2 PA0002    dnaN      DNA polymerase III, beta chain                
#>  3 PA0003    recF      RecF protein                                  
#>  4 PA0004    gyrB      DNA gyrase subunit B                          
#>  5 PA0005    lptA      lysophosphatidic acid acyltransferase, LptA   
#>  6 PA0006    NA        conserved hypothetical protein                
#>  7 PA0007    NA        hypothetical protein                          
#>  8 PA0008    glyS      glycyl-tRNA synthetase beta chain             
#>  9 PA0009    glyQ      glycyl-tRNA synthetase alpha chain            
#> 10 PA0010    tag       DNA-3-methyladenine glycosidase I             
#> # ℹ 5,703 more rows