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Cargo.toml

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+name = "fasta_extend"
+version = "0.1.0"
+edition = "2021"
+
+[dependencies]
+anyhow = "1.0.86"
+clap = { version = "4.5.16", features = ["derive"] }
+noodles-core = "0.15.0"
+noodles-fasta = "0.42.0"

src/main.rs

@@ -0,0 +1,108 @@
+use std::{fs::File, io::{self, BufReader}};
+
+use anyhow::Ok;
+use clap::Parser;
+use fasta::{
+    record::{Definition, Sequence},
+    Record,
+};
+use noodles_core::{Position, Region};
+use noodles_fasta as fasta;
+
+/// Simple program to greet a person
+#[derive(Parser, Debug)]
+#[command(version, about, long_about = None)]
+struct Args {
+    #[arg(short, long)]
+    fasta: String,
+
+    #[arg(short, long)]
+    reference: String,
+
+    #[arg(short, long)]
+    chr: String,
+
+    /// Position of first nt of fasta
+    #[arg(short, long)]
+    start: Option<usize>,
+
+    #[arg(short, long)]
+    end: Option<usize>,
+
+    #[arg(short, long)]
+    n: usize,
+
+    #[arg(short, long, default_value_t = false)]
+    left_anti_sens: bool,
+
+    #[arg(short = 'g', long, default_value_t = false)]
+    right_anti_sens: bool,
+}
+
+fn main() -> anyhow::Result<()> {
+    let args = Args::parse();
+
+    let mut reference_reader =
+        fasta::indexed_reader::Builder::default().build_from_path(&args.reference)?;
+
+    let mut sequences = Vec::new();
+    let mut regions = Vec::new();
+
+    if let Some(start) = args.start {
+        let (start, end) = if !args.left_anti_sens {
+            ( Position::try_from(start - args.n)?, Position::try_from(start - 1)?)
+        } else {
+            (Position::try_from(start + 1)?, Position::try_from(start + args.n)?)
+        };
+        let region = Region::new(args.chr.clone(), start..=end);
+        let sequence = reference_reader.query(&region)?.sequence().to_owned();
+        regions.push(format!("{}", region));
+        let sequence = if args.left_anti_sens {
+            sequence.complement().rev().collect::<Result<_, _>>()?
+        } else {
+            sequence
+        };
+        sequences.push(sequence);
+    }
+
+    let mut reader = File::open(&args.fasta)
+        .map(BufReader::new)
+        .map(fasta::io::Reader::new)?;
+
+    let record = reader.records().next().unwrap()?;
+    sequences.push(record.sequence().to_owned());
+    regions.push(String::from_utf8(record.name().to_vec())?);
+
+    if let Some(end) = args.end {
+        let (start, end) = if !args.right_anti_sens {
+            (Position::try_from(end + 1)?, Position::try_from(end + args.n)?)
+        } else {
+            (Position::try_from(end - args.n)?, Position::try_from(end - 1)?)
+        };
+        // let start = Position::try_from(end + 1)?;
+        // let end = Position::try_from(end + 1 + args.n)?;
+        let region = Region::new(args.chr.clone(), start..=end);
+        let sequence = reference_reader.query(&region)?.sequence().to_owned();
+        regions.push(format!("{}", region));
+        let sequence = if args.right_anti_sens {
+            sequence.complement().rev().collect::<Result<_, _>>()?
+        } else {
+            sequence
+        };
+        sequences.push(sequence);
+    }
+
+    let mut writer = fasta::io::writer::Builder::default().build_with_writer(io::stdout());
+
+    let sequence = sequences.iter().fold(Sequence::default(), |acc, seq| {
+        let mut merged_data = Vec::new();
+        merged_data.extend_from_slice(acc.as_ref());
+        merged_data.extend_from_slice(seq.as_ref());
+        Sequence::from(merged_data)
+    });
+
+    let record = Record::new(Definition::new(regions.join("_").replace(":", "_"), None), sequence);
+    writer.write_record(&record)?;
+
+    Ok(())
+}