feat: Add fa2fq and fq2fa conversion functions

Cargo.toml

@@ -42,4 +42,6 @@ log = "0.4"
 noodles-bam = "0.49.0"
 noodles-bgzf = "0.25"
 noodles-csi = "0.26"
+noodles-fasta = "0.30"
+noodles-fastq = "0.9"
 noodles-sam = "0.46"

src/fa2fq.rs

@@ -0,0 +1,25 @@
+use anyhow::Result;
+use noodles_fasta as fasta;
+use noodles_fastq as fastq;
+use std::path::Path;
+
+pub fn fa2fq<P: AsRef<Path>>(input: P) -> Result<()> {
+    let mut reader = fasta::reader::Builder.build_from_path(input)?;
+
+    let mut writer = fastq::Writer::new(std::io::stdout());
+
+    for result in reader.records() {
+        let record = result?;
+        let name = record.name().to_string();
+        let sequence = record.sequence().as_ref().to_vec();
+        let qualities = vec![b'@'; sequence.len()];
+        let fastq_record = fastq::Record::new(
+            fastq::record::Definition::new(name, ""),
+            sequence,
+            qualities,
+        );
+        writer.write_record(&fastq_record)?;
+    }
+
+    Ok(())
+}

src/fq2fa.rs

@@ -0,0 +1,26 @@
+use anyhow::Result;
+use noodles_fasta as fasta;
+use noodles_fastq as fastq;
+use std::path::Path;
+use std::{
+    fs::File,
+    io::{self, BufReader},
+};
+
+pub fn fq2fa<P: AsRef<Path>>(input: P) -> Result<()> {
+    let mut readerr = File::open(input)
+        .map(BufReader::new)
+        .map(fastq::Reader::new)?;
+
+    let mut writer = fasta::Writer::new(io::stdout());
+
+    for result in readerr.records() {
+        let record = result?;
+        let name = String::from_utf8(record.name().to_vec())?;
+        let sequence = fasta::record::Sequence::from(record.sequence().to_vec());
+        let fasta_record = fasta::Record::new(fasta::record::Definition::new(name, None), sequence);
+        writer.write_record(&fasta_record)?;
+    }
+
+    Ok(())
+}

src/main.rs

@@ -6,6 +6,8 @@ use log::LevelFilter;
 use std::path::PathBuf;
 
 mod extract;
+mod fa2fq;
+mod fq2fa;
 mod index;
 
 #[derive(Parser)]
@@ -38,6 +40,18 @@ enum Commands {
         /// Bam input file
         input: PathBuf,
     },
+
+    /// Convert a FASTA file to FASTQ
+    Fa2fq {
+        /// fasta input file
+        input: PathBuf,
+    },
+
+    /// Convert a FASTQ file to FASTA
+    Fq2fa {
+        /// fastq input file
+        input: PathBuf,
+    },
 }
 
 fn main() {
@@ -75,6 +89,14 @@ fn main() {
             info!("'index'  {input:?} ");
             index::index_bam(input).unwrap();
         }
+        Some(Commands::Fa2fq { input }) => {
+            info!("'fa2fq'  {input:?} ");
+            fa2fq::fa2fq(input).unwrap();
+        }
+        Some(Commands::Fq2fa { input }) => {
+            info!("'fq2fa'  {input:?} ");
+            fq2fa::fq2fa(input).unwrap();
+        }
 
         // If no subcommand was used, it's a normal top level command
         None => info!("No subcommand was used"),

tests/data/test_case1.fa

@@ -0,0 +1,4 @@
+>sequence1
+ATGCTAGCTAGCTAGCTAGCTAGCTA
+GCTAGCTAGCTAGCTAGCTAGCTAGC
+TAGCTAGCTAGCTAGCTAGCTAGCTA

tests/data/test_case1.fq

@@ -0,0 +1,4 @@
+@sequence1
+ATGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTA
++
+@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@