src/obikmer/src/cmd/phylo/tnt.rs

@@ -30,7 +30,8 @@ pub(super) fn write_sankoff_tnt(
     cost_scale: f64,
     free_loss: bool,
 ) {
-    let path = output.as_ref()
+    let path = output
+        .as_ref()
         .map(|p| format!("{}_sankoff.tnt", p.display()))
         .unwrap_or_else(|| "sankoff.tnt".into());
     let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
@@ -45,7 +46,11 @@ pub(super) fn write_sankoff_tnt(
 
     let n_sites = alignment.sequences.first().map(|s| s.len()).unwrap_or(0);
     writeln!(f, "xread").unwrap();
-    writeln!(f, "'obikmer central-position SNP families, calibrated Sankoff 16-state encoding'").unwrap();
+    writeln!(
+        f,
+        "'obikmer central-position SNP families, calibrated Sankoff 16-state encoding'"
+    )
+    .unwrap();
     writeln!(f, "{n_sites} {}", labels.len()).unwrap();
     for (label, seq) in labels.iter().zip(alignment.sequences.iter()) {
         write!(f, "{label} ").unwrap();
@@ -70,7 +75,12 @@ pub(super) fn write_sankoff_tnt(
     writeln!(f, "smatrix =0 (family16)").unwrap();
     for i in 0..16 {
         for j in (i + 1)..16 {
-            writeln!(f, "{}/{} {}", TNT_STATE_SYMBOL[i], TNT_STATE_SYMBOL[j], scaled_matrix[i][j]).unwrap();
+            writeln!(
+                f,
+                "{}/{} {}",
+                TNT_STATE_SYMBOL[i], TNT_STATE_SYMBOL[j], scaled_matrix[i][j]
+            )
+            .unwrap();
         }
     }
     writeln!(f, ";\n").unwrap();
@@ -83,7 +93,8 @@ pub(super) fn write_sankoff_tnt(
     // workflow is to `cd` into the output directory before `proc`-ing the
     // script, and an absolute path here would break if that directory is
     // later moved or copied elsewhere.
-    let tre_name = output.as_ref()
+    let tre_name = output
+        .as_ref()
         .and_then(|p| p.file_name())
         .map(|n| format!("{}_sankoff.tre", n.to_string_lossy()))
         .unwrap_or_else(|| "sankoff.tre".into());
@@ -97,21 +108,67 @@ pub(super) fn write_sankoff_tnt(
     // defaults below when the script is run. `;` ends a `quote` block like
     // any other TNT command, so the text itself must avoid semicolons.
     writeln!(f, "quote").unwrap();
-    writeln!(f, "Default search below (edit or delete this block to run your own strategy):").unwrap();
+    writeln!(
-    writeln!(f, "  hold N     : size of TNT's tree buffer (how many equally-parsimonious").unwrap();
+        f,
-    writeln!(f, "               trees it keeps in memory at once), 20 is a small, fast").unwrap();
+        "Default search below (edit or delete this block to run your own strategy):"
-    writeln!(f, "               default, raise it if mult reports it had to drop trees.").unwrap();
+    )
-    writeln!(f, "  mult       : traditional search (random addition sequences followed by").unwrap();
+    .unwrap();
-    writeln!(f, "               TBR branch-swapping, TNT's own default replication count),").unwrap();
+    writeln!(
-    writeln!(f, "               a reasonable first-pass strategy on this data's memory").unwrap();
+        f,
-    writeln!(f, "               footprint, xmult's ratchet/drift/tree-fusion buffers ran").unwrap();
+        "  hold N     : size of TNT's tree buffer (how many equally-parsimonious"
-    writeln!(f, "               this out of RAM at TNT's default mxram on this dataset.").unwrap();
+    )
-    writeln!(f, "  export - F : write the trees held in the buffer to file F, in").unwrap();
+    .unwrap();
-    writeln!(f, "               TNT/Hennig86 format ('-' means trees, as opposed to data).").unwrap();
+    writeln!(
+        f,
+        "               trees it keeps in memory at once), 20 is a small, fast"
+    )
+    .unwrap();
+    writeln!(
+        f,
+        "               default, raise it if mult reports it had to drop trees."
+    )
+    .unwrap();
+    writeln!(
+        f,
+        "  mult       : traditional search (random addition sequences followed by"
+    )
+    .unwrap();
+    writeln!(
+        f,
+        "               TBR branch-swapping, TNT's own default replication count),"
+    )
+    .unwrap();
+    writeln!(
+        f,
+        "               a reasonable first-pass strategy on this data's memory"
+    )
+    .unwrap();
+    writeln!(
+        f,
+        "               footprint, xmult's ratchet/drift/tree-fusion buffers ran"
+    )
+    .unwrap();
+    writeln!(
+        f,
+        "               this out of RAM at TNT's default mxram on this dataset."
+    )
+    .unwrap();
+    writeln!(
+        f,
+        "  export - F : write the trees held in the buffer to file F, in"
+    )
+    .unwrap();
+    writeln!(
+        f,
+        "               TNT/Hennig86 format ('-' means trees, as opposed to data)."
+    )
+    .unwrap();
     writeln!(f, ";").unwrap();
     writeln!(f, "hold 20;").unwrap();
     writeln!(f, "mult;").unwrap();
-    writeln!(f, "export - {tre_name};").unwrap();
+    writeln!(f, "taxname =;").unwrap();
+    writeln!(f, "tsave * {tre_name};").unwrap();
+    writeln!(f, "tsave /;").unwrap();
 
     info!(
         "TNT script → {path} (costs scaled x{cost_scale:.0}, runs a default `hold 20; mult;` \