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

Description Usage Arguments Value Examples

View source: R/read_fasta.R

Description

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

Usage

1
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

1
2
3
4
5
6
7
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 Feb. 6, 2018, noon