correctDomains: For all with the tool checked genomes, fCAT will save the...

In giangnguyen0709/fCAT: fCAT

Description

For all with the tool checked genomes, fCAT will save the domains of each genome into a domains file in the phyloprofile folder, which by default is the output folder in core directory or can be the folder specified by the user with the argument ppDir in the function checkCompleteness. When redo is on to recheck for a genome, whose pp exists already in the original pp, the tool must remove the lines of the genome from the original domains file. That is the purpose of this function

Usage

correctDomains(domainsFile, genome)

Arguments

domainsFile	path to the domains file
genome	name of the genome in the file, that should be remove

Value

none

Examples

#' ## Create a pseudo domains table
V1 <- c(
    "1001705at2759#1001705at2759|HUMAN@9606@3|Q15291|1",
    "551907at2759#551907at2759|AMPQU@400682@2|400682_0:001490|1"
)
V2 <- c(
    "1001705at2759|HOMSA@9606@2|9606_0:00004c",
    "551907at2759|AMPQU@400682@2|400682_0:001490|1"
)
V3 <- c(538, 1087)
V4 <- c("pfam_WD40", "flps_SINGLE_{G}")
V5 <- c(17, 1030)
V6 <- c(52, 1058)
V7 <- c(0.2265, 0.0936)
V8 <- c("Y", "Y")
domains <- data.frame(V1, V2, V3, V4, V5, V6, V7, V8)

## Write it in a file
wd <- getwd()
filePath <- paste(wd, "/fCAT_functiontest.domains", sep = "")
write.table(domains, filePath,
    sep = "\t", row.names = FALSE,
    quote = FALSE, col.names = FALSE
)

## correcting
correctDomains(filePath, "HUMAN@9606@3")

## Check if the file is corrected
read.table(filePath, sep = "\t", header = FALSE, comment.char = "")

## delete file
file.remove(filePath)

giangnguyen0709/fCAT documentation built on Feb. 10, 2021, 4:31 a.m.