faidx2seq: faidx2seq

In kullrich/distIUPAC: calculates IUPAC distances on Biostrings DNAStringSet and BStringSet objects

Description

This function returns a region of a bgzipped and samtools indexed fasta alignment file using samtools

Usage

faidx2seq(fasta, start = 1, end = NULL, format = "dna",
  samtools = "samtools")

Arguments

fasta	fasta file which needs to be indexed by 'samtools faidx'
start	region start [default: 1]
end	region end [default: NULL]
format	either dna or aa [default: "dna"]
samtools	path to samtools executable [default: "samtools"]

Author(s)

Kristian K Ullrich

Examples

fasta.gz.file<-system.file("extdata", "example.fasta.gz", 
  package="distIUPAC")
##complete alignment
dna<-faidx2seq(fasta.gz.file, format="dna", samtools="samtools")
##region from 5001 to 15000 from alignment
dna.region<-faidx2seq(fasta.gz.file, start = 5001, end = 15000,
  format = "dna", samtools = "samtools")

kullrich/distIUPAC documentation built on Jan. 9, 2020, 2:50 p.m.