Run GenomeTester4 Perl scripts with processx — gt4_run

Thin wrappers around Perl scripts bundled in inst/scripts.

Usage

gt4_run_script(script, args = character(), ...)

generate_vcf(args = character(), ...)

katk2vcf(args = character(), ...)

make_intersection(args = character(), ...)

make_union(args = character(), ...)

collate_repeats(args = character(), ...)

find_regions(args = character(), ...)

filter_collated(args = character(), ...)

filter_final(args = character(), ...)

unique_repeats(args = character(), ...)

Arguments

script: Relative script path under inst/scripts.
args: Character vector of command line arguments for the script.
...: Additional arguments passed to processx::run().

Value

A list from processx::run() with process results.

Examples

if (FALSE) { # \dontrun{
gt4_run_script("generate_vcf.pl", c("calls.txt"), error_on_status = FALSE)
} # }
if (FALSE) { # \dontrun{
generate_vcf(c("calls.txt"), error_on_status = FALSE)
} # }
if (FALSE) { # \dontrun{
katk2vcf(c("calls.txt"), error_on_status = FALSE)
} # }
if (FALSE) { # \dontrun{
make_intersection(c("list1", "list2"), error_on_status = FALSE)
} # }
if (FALSE) { # \dontrun{
make_union(c("list1", "list2"), error_on_status = FALSE)
} # }
if (FALSE) { # \dontrun{
collate_repeats(c("blast.tsv", "repeats.fa"), error_on_status = FALSE)
} # }
if (FALSE) { # \dontrun{
find_regions(c("overrep.tsv", "seq.fa", "100", "2"), error_on_status = FALSE)
} # }
if (FALSE) { # \dontrun{
filter_collated(c("groups.txt", "3"), error_on_status = FALSE)
} # }
if (FALSE) { # \dontrun{
filter_final(c("repeats.fa", "blast.tsv", "chr1"), error_on_status = FALSE)
} # }
if (FALSE) { # \dontrun{
unique_repeats(c("repeats.fa", "blast.tsv"), error_on_status = FALSE)
} # }