replace snaprank with snaptaxon

The new command can also snap to a list of given taxa.

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "umgap"
-version = "0.3.1"
+version = "0.3.2"
 authors = ["Felix Van der Jeugt <[email protected]>",
            "Stijn Seghers <[email protected]>",
            "Niels De Graef <[email protected]>",

src/args.rs

@@ -5,6 +5,7 @@ use std::path::PathBuf;
 use std::str::FromStr;
 
 use rank::Rank;
+use taxon::TaxonId;
 
 /// A reading frame
 #[allow(missing_docs)]
@@ -162,9 +163,9 @@ pub enum Opt {
 	#[structopt(name = "taxonomy")]
 	Taxonomy(Taxonomy),
 
-	/// Snap taxa to a specified rank.
-	#[structopt(name = "snaprank")]
-	SnapRank(SnapRank),
+	/// Snap taxa to a specified rank or one of the specified taxa.
+	#[structopt(name = "snaptaxon")]
+	SnapTaxon(SnapTaxon),
 
 	/// Interleaves a number of FASTQ files into a single FASTA output.
 	#[structopt(name = "fastq2fasta")]
@@ -443,12 +444,16 @@ pub struct FastqToFasta {
 	pub input: Vec<PathBuf>,
 }
 
-/// Snap taxa to a specified rank.
+/// Snap taxa to a specified rank or one of the specified taxa.
 #[derive(Debug, StructOpt)]
-pub struct SnapRank {
-	/// The rank to show
-	#[structopt(short = "r", long = "rank", default_value = "species")]
-	pub rank: Rank,
+pub struct SnapTaxon {
+	/// The rank to snap towards.
+	#[structopt(short = "r", long = "rank")]
+	pub rank: Option<Rank>,
+
+	/// A taxon to snap towards (allow multiple times).
+	#[structopt(short = "t", long = "taxons")]
+	pub taxons: Vec<TaxonId>,
 
 	/// Include invalidated taxa
 	#[structopt(short = "i", long = "invalid")]

src/main.rs

@@ -65,7 +65,7 @@ quick_main!(|| -> Result<()> {
 		args::Opt::Uniq(args)            => uniq(args),
 		args::Opt::FastqToFasta(args)    => fastq2fasta(args),
 		args::Opt::Taxonomy(args)        => taxonomy(args),
-		args::Opt::SnapRank(args)        => snaprank(args),
+		args::Opt::SnapTaxon(args)       => snaptaxon(args),
 		args::Opt::JsonTree(args)        => jsontree(args),
 		args::Opt::SeedExtend(args)      => seedextend(args),
 		args::Opt::Report(args)          => report(args),
@@ -483,18 +483,21 @@ fn taxonomy(args: args::Taxonomy) -> Result<()> {
 	 Ok(())
 }
 
-fn snaprank(args: args::SnapRank) -> Result<()> {
+fn snaptaxon(args: args::SnapTaxon) -> Result<()> {
 	let taxons = taxon::read_taxa_file(&args.taxon_file)?;
-	if args.rank == rank::Rank::NoRank {
+	if args.rank.map(|r| r == rank::Rank::NoRank).unwrap_or(false) {
 		return Err(ErrorKind::InvalidInvocation("Snap to an actual rank.".into()).into());
 	}
 
 	// Parsing the taxons
-	let tree	 = taxon::TaxonTree::new(&taxons);
-	let by_id	= taxon::TaxonList::new(taxons);
-	let snapping = tree.filter_ancestors(|tid|
-		by_id.get(tid).map(|t| t.rank == args.rank && (args.invalid || t.valid)).unwrap_or(false)
-	);
+	let tree = taxon::TaxonTree::new(&taxons);
+	let by_id = taxon::TaxonList::new(taxons);
+	let snapping = tree.filter_ancestors(|tid| {
+		args.taxons.contains(&tid) ||
+		by_id.get(tid)
+			.map(|t| (args.invalid || t.valid) && args.rank.map(|r| t.rank == r).unwrap_or(false))
+			.unwrap_or(false)
+	});
 
 	// Read and count taxon ranks
 	let stdin = io::stdin();