R: Reads the contents of nucleotide or protein FASTA file into a...

read_fasta {blaster} | R Documentation

## Reads the contents of nucleotide or protein FASTA file into a dataframe.

### Description

Reads the contents of nucleotide or protein FASTA file into a dataframe.

### Usage

    read_fasta(
      filename,
      filter = "",
      non_standard_chars = "error",
      alphabet = "nucleotide"
    )

### Arguments

`filename` | A string specifying the name of the FASTA file to be imported.
`filter` | An optional string specifying a sequence motif for sequence filtering. Only keeps those sequences containing this motif. Also splits the matched sequences and provides the split parts in two additional columns.
`non_standard_chars` | A string specifying instructions for handling non-standard nucleotide or amino acid characters. Options include 'remove', 'ignore' or throw an 'error'. Defaults to 'error'.
`alphabet` | A string specifying the query and database alphabet: 'nucleotide' or 'protein'. Defaults to 'nucleotide'.

### Value

A dataframe containing FASTA ids (Id column) and sequences (Seq column). If 'filter' is specified, the split sequences are stored in additional columns Part1 and Part2.

### Examples

    query <- system.file("extdata", "query.fasta", package = "blaster")

    query <- read_fasta(filename = query)

[Package blaster version 1.0.4 Index]