extract.traits: Apply rules to a set of detected genes

In ukaraoz/microtrait: microTrait

Apply rules to a set of detected genes

Description

Apply rules to a set of detected genes

Usage

## S3 method for class 'traits'
extract(
  in_file = system.file("extdata/genomic", "2695420375.fna", package = "microtrait",
    mustWork = TRUE),
  out_dir = system.file("extdata/genomic", package = "microtrait", mustWork = TRUE),
  type = "genomic",
  mode = "single",
  growthrate_predict = TRUE,
  optimalT_predict = TRUE,
  optimalT_predict_wtRNA = FALSE,
  save_tempfiles = F
)

Arguments

fasta_file

type out_dir

Value

extracted traits.

Examples

## Not run: in_file = system.file("extdata/examples/2619619645/in", "2619619645.genes.faa", package = "microtrait", mustWork = TRUE)
in_file = list(system.file("extdata/examples/2619619645/out", "2619619645.genes.faa.microtrait.domtblout", package = "microtrait", mustWork = TRUE),
               system.file("extdata/examples/2619619645/out", "2619619645.genes.faa.dbcan.domtblout", package = "microtrait", mustWork = TRUE))

## End(Not run)
## Not run: 
in_file = list(system.file("extdata/examples/2619619645/out", "2619619645.genes.faa.microtrait.domtblout", package = "microtrait", mustWork = TRUE),
               system.file("extdata/examples/2619619645/out", "2619619645.genes.faa.dbcan.domtblout", package = "microtrait", mustWork = TRUE))

## End(Not run)
type = "domtblout"

ukaraoz/microtrait documentation built on March 18, 2024, 5:47 p.m.