# Introduction to baseq

    library(baseq)

## Introduction

`baseq` is a basic sequence processing tool for biological data. It provides simple and efficient functions for common tasks in molecular biology, such as cleaning sequences, translating DNA/RNA to protein, and calculating GC content.

## Sequence Cleaning

You can clean DNA or RNA sequences by removing any non-standard characters. The universal `clean_seq()` function automatically detects the type.

    dna_seq <- "ATGCnNryMK"
    clean_seq(dna_seq)
    #> [1] "ATGC"

    rna_seq <- "AUGGCuuNnRYMK"
    clean_seq(rna_seq)
    #> [1] "AUGGCUU"

## Translation

`baseq` can translate DNA and RNA sequences into protein sequences in all six reading frames.

    dna_seq <- "ATCGAGCTAGCTAGCTAGCTAGCT"
    proteins <- dna_to_protein(dna_seq)
    proteins[["Frame F1"]]
    #> [1] "IELAS"

## GC Content

Calculate the GC content of a DNA sequence.

    dna_seq <- "ATGCATGC"
    gc_content(dna_seq)
    #> [1] 50

## Reading and Writing Files

`baseq` provides universal functions to read and write FASTA and FASTQ files.

    # Read a FASTA file into a dataframe
    # df <- read_seq("path/to/file.fasta")

    # Write a dataframe to a FASTA file
    # write_seq(df, "output.fasta")

For more details, see the documentation for individual functions.