Fasta Parser

Problem Description

Build a CLI tool fasta_stats that calculates the number of sequences for a provided fasta file and writes the results to a json file.

• Input argument: --fasta <file.fasta>
• Output argument: --outfile <outfile.json>

Expected command:

fasta_stats --fasta <file.fasta> --outfile <outfile.json>

Expected contents of output file:

#![allow(unused)]
fn main() {
{
    num_sequences: usize,
}
}

Checklist

• Define a struct for CLI arguments with clap.
• Define a struct FastaStats for storing calculated stats.
• Define a function get_fasta_stats that takes fasta: PathBuf and outfile: PathBuf as arguments.
  • Iterate over fasta records and keep track of num_sequences.
  • Store num_sequences in an instance of FastaStats
• Define a function write_json that writes the FastaStats instance to outfile.

Suggested Rust Crates

• Clap - argument parsing.
• Needletail - reading fasta files.
• Serde - serializing data.
• Serde json - serializing json.

Code Examples

• fasta_rs

Extra Credits

• Only allow input files with extensions .fasta, .fa, .fsa, .fna.
• Add more stats: average sequence length, average gc content and total number of bases.
• Graceful error handling.