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Grab bracken data and format to tibble.

Usage

read_bracken_file(filepath)

Arguments

filepath

Path to bracken .txt files.

Value

A tibble.

Examples

fpath <- system.file("extdata/bracken",
"7_S79_kraken2_report_bracken_output.txt", package = "bubbler")
read_bracken_file(fpath)
#> # A tibble: 221 × 8
#>    sample_id    name  taxonomy_id taxonomy_lvl kraken_assigned_reads added_reads
#>    <chr>        <chr>       <dbl> <chr>                        <dbl>       <dbl>
#>  1 7_S79_krake… Ente…        1352 S                             1733           0
#>  2 7_S79_krake… Ente…        1351 S                                8           0
#>  3 7_S79_krake… Ente…       53346 S                                3           0
#>  4 7_S79_krake… Ente…     2603296 S                                3           0
#>  5 7_S79_krake… Ente…      357441 S                                3           0
#>  6 7_S79_krake… Ente…        1354 S                                2           0
#>  7 7_S79_krake… Ente…       33945 S                                2           0
#>  8 7_S79_krake… Ente…       37734 S                                2           0
#>  9 7_S79_krake… Ente…       53345 S                                2           0
#> 10 7_S79_krake… Ente…        1353 S                                1           0
#> # ℹ 211 more rows
#> # ℹ 2 more variables: new_est_reads <dbl>, fraction_total_reads <dbl>