correctFasta: For every with the tool checked genomes, fCAT will save the...

In giangnguyen0709/fCAT: fCAT

Description

For every with the tool checked genomes, fCAT will save the sequences of each genome into a extended fasta 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 extended fasta file. That is the purpose of this function

Usage

correctFasta(fasta, genome)

Arguments

fasta	the path to the fasta file
genome	the name of the genome, that should be removed

Value

none

Examples

## Create pseudo extended fasta file
fasta <- c(
    ">1001705at2759|HUMAN@9606@3|Q15291|1",
    "MNLELLESFGQNYPEEADGTLDCISMALTCTFNRWGT",
    ">1489230at2759|ARATH@3702@2|3702_0:005bc2|1",
    "MAGRATIPARNSALIAMIADEDTVVGFLMAGVGNVDIRRKTNYLIVDS"
)

## Write it in a file in the current working directory
wd <- getwd()
filePath <- paste(wd, "/fCAT_functiontest.fa", sep = "")
writeLines(fasta, filePath)

## Correcting
correctFasta(filePath, "HUMAN@9606@3")

## Check if the file is corrected
fasta <- readLines(filePath)
print(fasta)

## Delete the file
file.remove(filePath)

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