Parse file

Parses files.

Usage

parse_file(fpath, pname, schemas_all, delim = "\t", ...)

Arguments

fpath

(character(1))
File path.

pname

(character(1))
Parser name (e.g. "breakends" - see docs).

schemas_all

(tibble())
Tibble with name, version and schema list-col.

delim

(character(1))
File delimiter.

...

Passed on to readr::read_delim.

Examples

path <- system.file("extdata/tool1", package = "nemo")
x <- Tool$new("tool1", pkg = "nemo", path)
schemas_all <- x$raw_schemas_all
pname <- "table1"
fpath <- file.path(path, "latest", "sampleA.tool1.table1.tsv")
(d <- parse_file(fpath, pname, schemas_all))
#> # A tibble: 3 × 7
#>   SampleID Chromosome Start   End metricX metricY metricZ
#>   <chr>    <chr>      <int> <int>   <dbl>   <dbl>   <dbl>
#> 1 sampleA  chr1          10    50     0.1     0.4     0.7
#> 2 sampleA  chr2         100   500     0.2     0.5     0.8
#> 3 sampleA  chr3        1000  5000     0.3     0.6     0.9