subset.fasta: Select a subset of sequences from a fasta file

Description Usage Arguments Value Author(s) Examples

View source: R/FastaUtils_functions.R

Description

This function loads a fasta file, selects a subset on sequences based on the sequence's names and writes a new fsata file.

Usage

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## S3 method for class 'fasta'
subset(file = NULL, subset = NULL, out = paste(file, ".subset", sep = ""))

Arguments

file

Fasta file

subset

Vector with (exact) names of the sequences to be retrieved.

out

Path to output file. If absent, the '.mod' is added to the input file's name (path is thus conserved).

Value

Writes a fasta file with the selected sequences.

Author(s)

Guillem Salazar <salazar@icm.csic.es>

Examples

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subset.fasta(file="http://greengenes.lbl.gov/Data/JD_Tutorial/UnAligSeq24606.txt",subset=c("24.6jsd1.Tut","24.6jsd2.Tut ","24.6jsd3.Tut "),out="out.fasta")

GuillemSalazar/FastaUtils documentation built on June 9, 2021, 7:26 p.m.