Fastx Toolkit

It is suggested that both excercises Fasta Parser and Fastq Filter are completed before proceeding.

Problem Description

Build a CLI tool fastx_toolkit for parsing and manipulating both fasta and fastq files.

Expected command:

fastx_toolkit <subcommand> --fastx <fastx_file> <optional args>.

Where subcommand can be:

• head - output the n first sequences.
• filter - filter sequences based on relevant metrics, such as length, gc_content, etc.
• sort - sort sequences based on length.

Checklist

• Figure out how Clap subcommands work.
• Define a dispatch function that, for given a subcommand, runs the correct function(s).
• Understand how needletail can be used to read a fasta or fastq file interchangably.
• Define common functions for reading/writing results.

Suggested Rust Crates

• Clap - argument parsing.
• Needletail - reading fasta files.

Code Examples

• fasta_rs
• fastq_rs

Extra Credits

• Only allow input files with extensions .fasta, .fa, .fsa, .fna, .fastq, .fastq.gz.
• Graceful error handling.
• Replacing Needletail with Bio + Rayon to enable multi-threading.