filterFasta: Filter fasta file by target chromosomes
In HatsuneCode/TrustVDJ: Tools for Immune Repertoire Analysis

filterFasta

R Documentation

Filter fasta file by target chromosomes

Description

filterFasta reads fasta file and filter it by target chromosomes. (.gz supported)

Usage

filterFasta(
  fasta,
  chromosomes = NULL,
  out = NULL,
  sep = "\\s",
  verbose = TRUE
)

Arguments

`fasta`	character. Path to fasta file.
`chromosomes`	character. Target chromosomes.
`out`	character. Output file.
`sep`	character. Fasta name separator. Default `\s`
`verbose`	logical. Print progress. Default `TRUE`

Value

if success, return TRUE

Examples

fa = system.file('extdata', 'IMGT_Homo_sapiens.fa.gz', package = 'TrustVDJ')
filterFasta(fa, c('IGHD1-1*01', 'TRDD1*01'), 'filter.fa')
fa = readLines('filter.fa')
file.remove('filter.fa')
cat(paste(fa, '\n', collapse = ''))

HatsuneCode/TrustVDJ documentation built on Aug. 13, 2022, 9:36 p.m.