read_fasta: Read a FASTA file into a tidy dataframe. Wrapper around...

In marcottelab/pepliner: MS Data Visualization

Description

Read a FASTA file into a tidy dataframe. Wrapper around seqinr::read.fasta

Usage

read_fasta(fasta_filename, annot = FALSE)

Arguments

fasta_filename	FASTA file from which the sequences will be extracted.
annot	If TRUE, extract sequence ID annotation into its own column
...	Unused extra arguments

Value

A tidy data.frame with one column for ID and one column for sequence.

ID	Sequence header from FASTA '>ID'
Sequence	Corresponding sequence, any bioalphabet (RNA/DNA/etc)
Annot	Full annotated FASTA header '>ID info|info|info'

Examples

test.fasta is a FASTA formatted file for ex:
   > GENENAME1
   atgctgacgta
   agctacagtat
   cagctactaag
read_fasta("test.fasta")
read_fasta("test.fasta", annot=TRUE)

marcottelab/pepliner documentation built on May 21, 2019, 8:05 a.m.