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fix: marginal reconstruction needs use the most likely state, not the… #305

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Jan 2, 2025
Merged

fix: marginal reconstruction needs use the most likely state, not the… #305

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31 changes: 9 additions & 22 deletions packages/treetime/src/commands/ancestral/marginal_sparse.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -414,10 +414,12 @@ pub fn ancestral_reconstruction_marginal_sparse(
return;
}

dbg!(&node.payload.name);
let seq: Seq = (0..n_partitions)
.flat_map(|si| {
let PartitionLikelihood { alphabet, .. } = &partitions[si];
let node_seq = &node.payload.sparse_partitions[si].seq;
let node_profile = &node.payload.sparse_partitions[si].profile;

let mut seq = if node.is_root {
node_seq.sequence.clone()
Expand All @@ -433,11 +435,6 @@ pub fn ancestral_reconstruction_marginal_sparse(
seq[m.pos()] = m.qry();
}

// Implant most likely state of variable sites
for (&pos, states) in &node.payload.sparse_partitions[si].seq.fitch.variable {
seq[pos] = states.get_one();
}

// Implant indels
for indel in &edge.indels {
if indel.deletion {
Expand All @@ -456,8 +453,10 @@ pub fn ancestral_reconstruction_marginal_sparse(
seq[r.0..r.1].fill(ambig_char);
}

for (pos, states) in &node_seq.fitch.variable {
seq[*pos] = states.get_one();
// change variable sites to their most likely state
for (pos, states) in &node_profile.variable {
dbg!(pos, &states);
seq[*pos] = alphabet.char(states.dis.argmax().unwrap());
}

node.payload.sparse_partitions[si].seq.sequence = seq.clone();
Expand Down Expand Up @@ -501,16 +500,10 @@ mod tests {

let aln = read_many_fasta_str(
indoc! {r#"
>root
ACAGCCATGTATTG--
>AB
ACATCCCTGTA-TG--
>A
ACATCGCCNNA--GAC
>B
GCATCCCTGTA-NG--
>CD
CCGGCCATGTATTG--
>C
CCGGCGATGTRTTG--
>D
Expand All @@ -522,11 +515,11 @@ mod tests {
let expected = read_many_fasta_str(
indoc! {r#"
>root
ACAGCCATGTATTG--
TCGGCGCTGTATTG--
>AB
ACATCCCTGTA-TG--
ACATCGCTGTA-TG--
>CD
CCGGCCATGTATTG--
TCGGCGGTGTATTG--
"#},
&NUC_ALPHABET,
)?
Expand Down Expand Up @@ -570,16 +563,10 @@ mod tests {

let aln = read_many_fasta_str(
indoc! {r#"
>root
ACAGCCATGTATTG--
>AB
ACATCCCTGTA-TG--
>A
ACATCGCCNNA--GAC
>B
GCATCCCTGTA-NG--
>CD
CCGGCCATGTATTG--
>C
CCGGCGATGTRTTG--
>D
Expand Down
5 changes: 1 addition & 4 deletions test_scripts/ancestral_sparse.py
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Original file line number Diff line number Diff line change
Expand Up @@ -224,11 +224,8 @@ def ancestral_sparse(graph: Graph) -> float:
return logLH

def tests():
aln = {"root":"ACAGCCATGTATTG--",
"AB":"ACATCCCTGTA-TG--",
"A":"ACATCGCCNNA--GAC",
aln = {"A":"ACATCGCCNNA--GAC",
"B":"GCATCCCTGTA-NG--",
"CD":"CCGGCCATGTATTG--",
"C":"CCGGCGATGTRTTG--",
"D":"TCGGCCGTGTRTTG--"}

Expand Down