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Push zpwxxpnpktps #67

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coissac merged 46 commits from push-zpwxxpnpktps into main 2026-08-17 09:41:42 +00:00
Conversation 0 Commits 46 Files Changed 405
+73 -16
1 changed files with 73 additions and 16 deletions
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Showing only changes of commit 53c40b7a53 - Show all commits
src/obikmer/src/cmd/phylo/tnt.rs
+73 -16
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@@ -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!(f, " hold N : size of TNT's tree buffer (how many equally-parsimonious").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,
"Default search below (edit or delete this block to run your own strategy):"
)
.unwrap();
writeln!(
f,
" hold N : size of TNT's tree buffer (how many equally-parsimonious"
)
.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;` \