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Abandoning rapidNJ Newick to vector conversion for now
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@jhellewell14
jhellewell14 committed Apr 17, 2024
1 parent 39922e5 commit 2f3be0c
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Showing 2 changed files with 93 additions and 90 deletions.
39 changes: 4 additions & 35 deletions src/lib.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,6 @@ use regex::{RegexSet, RegexSetBuilder};
use crate::dspsa::hill_peturb;
use crate::gen_list::*;
use crate::newick::newick_to_vec;
use crate::newick::parse_rapidNJ_newick;
use crate::phylo2vec::*;
use crate::tree::Tree;
use crate::likelihoods::logse;
Expand All @@ -33,37 +32,7 @@ pub mod cli;
use crate::cli::*;

pub fn main() {
let args = cli_args();
// Newick string example
// let nstr: String = String::from("(((((('9':0.00066056,'4':0.0012556):0.00030238,('25':0.00042479,'19':0.00030083):0.00039731):0.00012351,'7':0.00039526):8.5797e-05,'18':0.00068249):0.00011977,'20':0.00056004):9.6199e-05,(((((((('17':0.0045802,'8':0.0021951):0.00019116,(((('24':0.0021162,'12':0.0017684):0.00074803,'13':0.0043482):0.00026831,('27':0.00063335,'5':0.00071804):0.0024273):4.8521e-05,((('23':0.0012435,'2':0.0012676):0.00011672,('21':0.00085695,'6':0.00096101):0.001509):0.00046989,'10':0.0020611):0.00092726):0.00022606):0.00019029,'26':0.0027488):0.00030355,('14':0.0021462,'0':0.0018751):0.00061029):0.00035469,'1':0.00096653):0.00015559,'22':0.0013558):7.0943e-05,('16':0.00054383,'15':0.00076666):0.00015841):0.00016779,'11':0.0021712):9.9157e-05,'3':0.00081132);");
let nstr: String = String::from("(('7':0.00064945,'3':0.00085552):5.9503e-05,('9':0.00060885,'4':0.0013073):0.00019161,((((('6':0.0023043,'2':0.0011704):0.0017225,'5':0.0035144):8.4584e-05,'8':0.0024813):0.0002661,'0':0.0023835):0.00062217,'1':0.00096265):0.00052941);");
let mut x: String = parse_rapidNJ_newick(&nstr);
println!("{:?}", x);


// Need to add a ( after the correct , heading in from the left
// Then another ) just before the ; at the end
let mut brack_count = 0;
let mut add_ind: usize = 0;
for (ind, el) in x.char_indices() {
// println!("{:?}", el);
if el.eq(&'('){
brack_count += 1;
} else if el.eq(&')') {
brack_count -= 1;
} else if el.eq(&',') && brack_count.eq(&1) {
add_ind = ind;
break;
}
// println!("{brack_count}");
}
// println!("{add_ind}");

x.insert(add_ind + 1, '(');
x.insert(x.len() - 1, ')');
println!("{:?}", x);

println!("{:?}", newick_to_vec(&x, 27));
let args = cli_args();

// Define rate matrix
let q: na::Matrix4<f64> = na::Matrix4::new(
Expand All @@ -80,9 +49,9 @@ pub fn main() {

tr.update_likelihood_postorder(&q);

// println!("{}", tr.get_tree_likelihood());
// println!("{:?}", tr.newick());
// println!("{:?}", tr.tree_vec);
println!("{}", tr.get_tree_likelihood());
println!("{:?}", tr.newick());
println!("{:?}", tr.tree_vec);

if !args.no_optimise {
// tr.hillclimb(&q, 100);
Expand Down
144 changes: 89 additions & 55 deletions src/newick.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -16,61 +16,95 @@ pub fn newick_to_vec(nw: &String, n_leaves: usize) -> Vec<usize>{
y
}

pub fn parse_rapidNJ_newick(nw: &String) -> String {
// Newick string example
// let nstr: String = String::from("(((((('9':0.00066056,'4':0.0012556):0.00030238,('25':0.00042479,'19':0.00030083):0.00039731):0.00012351,'7':0.00039526):8.5797e-05,'18':0.00068249):0.00011977,'20':0.00056004):9.6199e-05,(((((((('17':0.0045802,'8':0.0021951):0.00019116,(((('24':0.0021162,'12':0.0017684):0.00074803,'13':0.0043482):0.00026831,('27':0.00063335,'5':0.00071804):0.0024273):4.8521e-05,((('23':0.0012435,'2':0.0012676):0.00011672,('21':0.00085695,'6':0.00096101):0.001509):0.00046989,'10':0.0020611):0.00092726):0.00022606):0.00019029,'26':0.0027488):0.00030355,('14':0.0021462,'0':0.0018751):0.00061029):0.00035469,'1':0.00096653):0.00015559,'22':0.0013558):7.0943e-05,('16':0.00054383,'15':0.00076666):0.00015841):0.00016779,'11':0.0021712):9.9157e-05,'3':0.00081132);");
// let mut nstr: String = String::from("(('7':0.00064945,'3':0.00085552):5.9503e-05,('9':0.00060885,'4':0.0013073):0.00019161,((((('6':0.0023043,'2':0.0011704):0.0017225,'5':0.0035144):8.4584e-05,'8':0.0024813):0.0002661,'0':0.0023835):0.00062217,'1':0.00096265):0.00052941);");
// println!("{:?}", nstr);
// First we need to root the rapidNJ tree
// nstr = root_newick(nstr);

// let mut x: String = parse_rapidNJ_newick(&nstr);
// println!("{:?}", x);
// let y: Vec<&str> = x.rsplitn(3, ')').collect();
// println!("{:?}", y);

// pub fn root_newick(mut nstr: String) -> String {
// // To root, we need to add a ( after the correct , heading in from the left
// // Then add another ) just before the ; at the end
// let mut brack_count = 0;
// let mut add_ind: usize = 0;
// for (ind, el) in nstr.char_indices() {
// if el.eq(&'('){
// brack_count += 1;
// } else if el.eq(&')') {
// brack_count -= 1;
// } else if el.eq(&',') && brack_count.eq(&1) {
// add_ind = ind;
// break;
// }
// }
// nstr.insert(add_ind + 1, '(');
// nstr.insert(nstr.len() - 1, ')');
// println!("{:?}", nstr);
// nstr
// }

// pub fn parse_rapidNJ_newick(nw: &String) -> String {

// Chop the Newick string into nodes
let v: Vec<&str> = nw.split_inclusive(|c: char| c.eq(&')') || c.eq(&','))
.filter(|s| !s.is_empty() && s.ne(&";"))
.collect();

// Initiate data structures
let n_nodes = v.len();
let mut branch_len: Vec<f64> = Vec::with_capacity(n_nodes);
let mut name_dict: HashMap<usize, String> = HashMap::with_capacity(n_nodes);
let mut node_index: usize = 0;
let mut new_newick: Vec<String> = Vec::with_capacity(n_nodes);

// Iterate over nodes
for node in v {
// Cut outbrackets and commas
let cleaned_node: String = node.replace(&['(', '\'', ')', ','], "");

// Split into label and branch length
let split_node: Vec<&str> = cleaned_node.split(':').collect();

// Get old node label (an old label is assigned if no previous
// label due to being internal node)
let node_name: String = match split_node[0].is_empty() {
true => node_index.to_string(),
false => split_node[0].to_string(),
};
// Put into name HashMap
name_dict.insert(node_index, node_name);

// Get branch length
let blen: f64 = split_node[1].parse().unwrap();
branch_len.push(blen);

// Put new node labels into old newick string
if split_node[0].is_empty() {
let new_el: String = node.replace(":", &format!("{}{}", node_index.to_string(), ":"));
new_newick.push(new_el);

} else {
let new_el: String = node.replace(&format!("'{}'", name_dict.get(&node_index).unwrap()),
&format!("{}", node_index.to_string()));
new_newick.push(new_el);
}

// Iterate node index
node_index += 1;
}
// // Chop the Newick string into nodes
// let v: Vec<&str> = nw.split_inclusive(|c: char| c.eq(&')') || c.eq(&','))
// .filter(|s| !s.is_empty() && s.ne(&";"))
// .collect();

// // Initiate data structures
// let n_nodes = v.len();
// let mut branch_len: Vec<f64> = Vec::with_capacity(n_nodes);
// let mut name_dict: HashMap<usize, String> = HashMap::with_capacity(n_nodes);
// let mut node_index: usize = 0;
// let mut new_newick: Vec<String> = Vec::with_capacity(n_nodes);

// // Iterate over nodes
// for node in v {
// // Cut outbrackets and commas
// let cleaned_node: String = node.replace(&['(', '\'', ')', ','], "");

// // Split into label and branch length
// let split_node: Vec<&str> = cleaned_node.split(':').collect();

// // Get old node label (an old label is assigned if no previous
// // label due to being internal node)
// let node_name: String = match split_node[0].is_empty() {
// true => node_index.to_string(),
// false => split_node[0].to_string(),
// };
// // Put into name HashMap
// name_dict.insert(node_index, node_name);

// // Get branch length
// let blen: f64 = split_node[1].parse().unwrap();
// branch_len.push(blen);

// // Put new node labels into old newick string
// if split_node[0].is_empty() {
// let new_el: String = node.replace(":", &format!("{}{}", node_index.to_string(), ":"));
// new_newick.push(new_el);

// } else {
// let new_el: String = node.replace(&format!("'{}'", name_dict.get(&node_index).unwrap()),
// &format!("{}", node_index.to_string()));
// new_newick.push(new_el);
// }

// // Iterate node index
// node_index += 1;
// }

// Put newick string with new labels together
let mut new_str: String = new_newick.join("");
new_str.push_str(&node_index.to_string());
new_str.push_str(":0.0001");
new_str.push_str(";");
// // Put newick string with new labels together
// let mut new_str: String = new_newick.join("");
// new_str.push_str(")");
// new_str.push_str(&node_index.to_string());
// new_str.push_str(":0.0001");
// new_str.push_str(";");

new_str
}
// new_str
// }

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