feat: add gap character validation for input sequences in build command

CHANGELOG.md

@@ -1,6 +1,6 @@
 ## Unreleased
 
-- updated Rust version to 1.90 (see #168) and dependencies (see #169)
+- add more informative error message for the `build` command when input sequences contain gap characters, see #172.
 
 ## 1.2.1
 

packages/pangraph/src/commands/build/build_run.rs

@@ -8,7 +8,7 @@ use crate::pangraph::strand::Strand::Forward;
 use crate::tree::clade::postorder;
 use crate::tree::neighbor_joining::build_tree_using_neighbor_joining;
 use crate::utils::progress_bar::ProgressBar;
-use crate::{make_internal_error, make_internal_report};
+use crate::{make_error, make_internal_error, make_internal_report};
 use color_eyre::owo_colors::{AnsiColors, OwoColorize};
 use color_eyre::{Help, SectionExt};
 use eyre::{Report, WrapErr};
@@ -67,6 +67,9 @@ pub fn build_run(args: &PangraphBuildArgs) -> Result<(), Report> {
 
   let fastas = read_many_fasta(input_fastas)?;
 
+  // Ensure that no input sequences contain gap characters
+  ensure_no_gap_characters(&fastas)?;
+
   // TODO: adjust fasta letter case if `upper_case` is set
   // TODO: check for duplicate fasta names
 
@@ -79,6 +82,33 @@ pub fn build_run(args: &PangraphBuildArgs) -> Result<(), Report> {
   Ok(())
 }
 
+/// Ensure that no input sequences contain gap characters (`-`).
+/// If any sequences with gaps are found, an error is returned listing the offending sequences.
+fn ensure_no_gap_characters(fastas: &[FastaRecord]) -> Result<(), Report> {
+  let sequences_with_gaps: Vec<&str> = fastas
+    .iter()
+    .filter_map(|record| record.seq.contains_str("-").then_some(record.seq_name.as_str()))
+    .collect();
+
+  if sequences_with_gaps.is_empty() {
+    return Ok(());
+  }
+
+  let names_listing = sequences_with_gaps.iter().join("\n");
+
+  make_error!(
+    "Detected gap character '-' in {} input sequences: {}. Pangraph does not support gap characters in the input.",
+    sequences_with_gaps.len(),
+    names_listing
+  )
+  .with_section(|| names_listing.header("Sequences containing gaps:"))
+  .with_section(|| {
+    "Remove gap characters from the input FASTA before running `pangraph build`."
+      .color(AnsiColors::Cyan)
+      .header("Suggestion:")
+  })
+}
+
 pub fn build(fastas: Vec<FastaRecord>, args: &PangraphBuildArgs, verify: bool) -> Result<Pangraph, Report> {
   // If verification is requested, we need to keep a copy of the original FASTA records
   // to compare them with the sequences reconstructed from the graph.
@@ -171,3 +201,39 @@ pub fn build(fastas: Vec<FastaRecord>, args: &PangraphBuildArgs, verify: bool) -
 
   Ok(graph)
 }
+
+#[cfg(test)]
+mod tests {
+  use super::*;
+  use crate::representation::seq::Seq;
+
+  #[test]
+  fn ensure_no_gap_characters_accepts_clean_sequences() {
+    let record = FastaRecord {
+      seq_name: "clean_seq".to_owned(),
+      seq: Seq::from_str("AACCGGTT"),
+      ..Default::default()
+    };
+
+    ensure_no_gap_characters(std::slice::from_ref(&record)).unwrap();
+  }
+
+  #[test]
+  fn ensure_no_gap_characters_rejects_sequences_with_gaps() {
+    let clean = FastaRecord {
+      seq_name: "clean".to_owned(),
+      seq: Seq::from_str("ACGT"),
+      ..Default::default()
+    };
+
+    let gappy = FastaRecord {
+      seq_name: "gappy".to_owned(),
+      seq: Seq::from_str("AC-GT"),
+      ..Default::default()
+    };
+
+    let fastas = vec![clean, gappy];
+
+    assert!(ensure_no_gap_characters(&fastas).is_err());
+  }
+}