loadFasta: Read or write a FASTA File

In robertdouglasmorrison/DuffyTools: Duffy Lab Utility Tools

Read or write a FASTA File

Description

Read/write a FASTA file from/to disk

Usage

loadFasta( file = "file.fasta", verbose = TRUE, short.desc = TRUE)
writeFasta( fasta, file = NULL, line.width = 80)
writeLongFasta( desc, seq, file = NULL)

Arguments

file	complete path name to an existing FASTA file for loadFasta, or new file name for writing
short.desc	logical, should the descriptor text be truncated at the first blank character
fasta	a fasta object, with 'desc' and 'seq' named elements
desc	character vector of descriptors
seq	character vector of sequences
line.width	integer value, the maximum line wrap length for written FASTA files

Details

loadFasta is a wrapper around the Biostrings function 'readBStringSet'.

The 'LongFasta' is a faster version that bypasses the line wrapping step, writing the entire sequence on a single line

Value

For loadFasta, a list of length 2, with:

desc	character vector of descriptors, from the '>' lines of the FASTA file
seq	character vector of sequences

See Also

as.Fasta for making fasta objects getFastaSeqFromFilePath, for getting the genomic sequence for a specific chrmosome.

robertdouglasmorrison/DuffyTools documentation built on May 6, 2024, 8:26 p.m.