Parses files.
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$new("tool1", pkg = "nemo", path)
schemas_all <- x$config$get_schemas_raw()
f <- function(ver, tbl) file.path(path, ver, paste0("sampleA.tool1.", tbl, ".tsv"))
# table1: three versions with different column sets
(d1_v123 <- parse_file(f("v1.2.3", "table1"), "table1", schemas_all))
#> # A tibble: 3 × 5
#> SampleID Chromosome Start End metricX
#> <chr> <chr> <int> <int> <dbl>
#> 1 sampleA chr1 10 50 0.1
#> 2 sampleA chr2 100 500 0.2
#> 3 sampleA chr3 1000 5000 0.3
(d1_v456 <- parse_file(f("v4.5.6", "table1"), "table1", schemas_all))
#> # A tibble: 3 × 4
#> SampleID Chromosome Start End
#> <chr> <chr> <int> <int>
#> 1 sampleA chr1 10 50
#> 2 sampleA chr2 100 500
#> 3 sampleA chr3 1000 5000
(d1_lat <- parse_file(f("latest", "table1"), "table1", schemas_all))
#> # A tibble: 3 × 6
#> SampleID Chromosome Start End metricY metricZ
#> <chr> <chr> <int> <int> <dbl> <dbl>
#> 1 sampleA chr1 10 50 0.4 0.7
#> 2 sampleA chr2 100 500 0.5 0.8
#> 3 sampleA chr3 1000 5000 0.6 0.9
# table2: two versions (v1.0.0 drops metricB)
(d2_v1 <- parse_file(f("v1.0.0", "table2"), "table2", schemas_all))
#> # A tibble: 3 × 2
#> SampleID metricA
#> <chr> <chr>
#> 1 sampleA a
#> 2 sampleA b
#> 3 sampleA c
(d2_lat <- parse_file(f("latest", "table2"), "table2", schemas_all))
#> # A tibble: 3 × 3
#> SampleID metricA metricB
#> <chr> <chr> <dbl>
#> 1 sampleA a 12.3
#> 2 sampleA b 4.56
#> 3 sampleA c 7.89