Fasta CLI Toolkit

A small CLI toolkit for interacting with fasta files developed in Rust.

As of 2022-08-29 there are no checks on wether the file is actually a fasta file, since it's a plain text file.

TODO

I won't set any specific dates because I'm doing this on my free time.

• DNA to Amino acid translation (It's actually RNA, but can be worked around easily now)
• DNA transcrption and translation
• Amino Acid generation

---

Down here harder things, to my assesment

• Alignement between two sequences I'd rather do Smith-Waterman first, feels easier Then someday I'll make Needleman-Wunsch
• Blastn ----> Through NCBI database?

Syntax

Printing files

Reads the file and outputs its contents

$ fasta_cli_toolkit print /path/to/file

Cutting sequences

Reads the file into a Fasta struct, then cuts the sequence, and writes to ouput file

$ fasta_cli_toolkit cut start end /path/to/input/file /path/to/output/file

Format

Reads the file into a Fasta struct, formats using TextWrap, and outputs the formatted text. If output file is provided, writes it.

$ fasta_cli_toolkit format /path/to/input/file [/path/to/output/file]

Generate

Generates a random DNA sequence long N lines and writes it to output file.

$ fasta_cli_toolkit generate N /path/to/output/file [-r|--rna]

Use the -r or --rna options to generate a RNA sequence

Analyze

Prints a summary of the sequence:

• Number of bases
• AT Count & Percentage
• GC Count & Percentage

$ fasta_cli_toolkit analyze /path/to/file

Get

Get subcommands:

• complementary: Gets the complementary strand of the given sequence

  $ fasta_cli_toolkit get complementary /path/to/file [/path/to/output/file]

• reverse Gets the reverse strand of the given sequence

  $ fasta_cli_toolkit get reverse /path/to/file [/path/to/output/file]

• revcomp Gets the reverse-complementary strand of the given sequence

  $ fasta_cli_toolkit get revcomp /path/to/file [/path/to/output/file]