Adjust tests and test data for newick parser

Adjusted tests and test data for newick parser to never use number-only IDs for nodes and
to use internal node id generator for comparison.

Author: junniest

phylo/data/p105.msa.fa

@@ -1,18 +1,18 @@
->284813
+>s284813
 --------------------------------------------QRLIL-----------
 ---------------------------------
->284811
+>s284811
 -MSDL--E----HESVPK--IPNESVWPDIVYLPDFKPTFPKWQ----------------
 ---------------------------------
->284593
+>s284593
 MSSELPGE----HESIPK--IPSEAVWPDIVYLPDFKPSFPQWR----------------
 ---------------------------------
->237561
+>s237561
 -MVET--E----HESIPQ--MPNEEIWPDVNYLPDFKSSFPQWK----------------
 ----------NDDRDHNNYNEDNIGIDKHQNM-
->284591
+>s284591
 -MVDT--E----HESISP--MPTEETWPGVTALPDYKPTFPQWS-----VGTNMKSGYNA
 AAGPGLMMST-----------------------
->284812
+>s284812
 -------ERSNC-DRISETGLPNEEVWPGVTLLQDYKSTFPRWK----------------
 --------------------------------F

phylo/data/p105.newick

@@ -1 +1 @@
-((284811:0.0000000000000002220446049250313,(284593:0.09695146373489569,(237561:0.3249811214954128,(284812:0.2932969786389556,(284813:4183.274915114282,284591:0.16527960508898415):0.16533876806006598):0.04817830194688745):0.10198380019982661):0.041663718143987165):0);
+((s284811:0.0000000000000002220446049250313,(s284593:0.09695146373489569,(s237561:0.3249811214954128,(s284812:0.2932969786389556,(s284813:4183.274915114282,s284591:0.16527960508898415):0.16533876806006598):0.04817830194688745):0.10198380019982661):0.041663718143987165):0);

phylo/src/optimisers/blen_optimiser_tests.rs

@@ -143,10 +143,10 @@ fn repeated_optimisation_limit() {
 
 #[test]
 fn only_gap_sequence() {
-    let tree = tree!("((5207:0.8699783346462397,284812:226000000):0);");
+    let tree = tree!("((l5207:0.8699783346462397,l284812:226000000):0);");
     let msa: MSA = Alignment::from_aligned(
         Sequences::with_alphabet(
-            vec![record!("284812", b"-"), record!("5207", b"V")],
+            vec![record!("l284812", b"-"), record!("l5207", b"V")],
             Alphabet::protein(),
         ),
         &tree,

phylo/src/pip_model/tests.rs

@@ -830,16 +830,16 @@ fn blen_leading_to_small_probs() {
 
 #[test]
 fn blen_leading_to_minusinf() {
-    let tree = tree!("((284811:0.0000000000000002,(284593:0.1,(237561:0.3,(284812:0.3,(284813:400.9,284591:0.2):40000000000000.2):0.05):0.1):0.04):0);");
+    let tree = tree!("((s284811:0.0000000000000002,(s284593:0.1,(s237561:0.3,(s284812:0.3,(s284813:400.9,s284591:0.2):40000000000000.2):0.05):0.1):0.04):0);");
     let msa = MSA::from_aligned(
         Sequences::with_alphabet(
             vec![
-                record!("284813", b"-"),
-                record!("284811", b"W"),
-                record!("284593", b"W"),
-                record!("237561", b"W"),
-                record!("284591", b"W"),
-                record!("284812", b"W"),
+                record!("s284813", b"-"),
+                record!("s284811", b"W"),
+                record!("s284593", b"W"),
+                record!("s237561", b"W"),
+                record!("s284591", b"W"),
+                record!("s284812", b"W"),
             ],
             Alphabet::protein(),
         ),

phylo/src/tree/nj_builder.rs

@@ -272,8 +272,8 @@ mod tests {
         LevenshteinDNACorrected as LDNACorr, LevenshteinProteinCorrected,
     };
     use crate::random::{FakeGenerator, FakeRng};
-    use crate::tree::Node;
     use crate::tree::NodeIdx::{self, Internal as I, Leaf as L};
+    use crate::tree::{generate_internal_node_id as gen_id, Node};
     use crate::{record_wo_desc as record, tree};
 
     use super::*;
@@ -338,13 +338,17 @@ mod tests {
                 17.0, 14.0, 11.0, 12.0, 10.0, 13.0, 8.0, 0.0;
             ],
         };
-        let sequences = Sequences::new((1..=8).map(|i| record!(&i.to_string(), b"")).collect());
+        let sequences = Sequences::new(
+            (1..=8)
+                .map(|i| record!(format!("s{}", i).as_str(), b""))
+                .collect(),
+        );
         let mut rng = FakeGenerator::default();
         let nj_tree = NJTreeBuilder::new(LDNACorr {})
             .build_from_distances(nj_distances, &sequences, &mut rng)
             .unwrap();
         let correct_tree =
-            tree!("((8:6,7:2):0.5,((5:1,6:4):2,(4:3,(3:1,(1:5,2:2):2):1):2):0.5):0.0;");
+            tree!("((s8:6,s7:2):0.5,((s5:1,s6:4):2,(s4:3,(s3:1,(s1:5,s2:2):2):1):2):0.5):0.0;");
         assert_eq!(nj_tree.length, correct_tree.length);
         for leaf in nj_tree.leaves() {
             assert_eq!(leaf.blen, correct_tree.by_id(&leaf.id).blen);
@@ -480,10 +484,10 @@ mod tests {
             Node::new_leaf(2, Some(I(7)), 4.0, "C2".to_string()),
             Node::new_leaf(3, Some(I(6)), 2.0, "D3".to_string()),
             Node::new_leaf(4, Some(I(6)), 1.0, "E4".to_string()),
-            Node::new_internal(5, Some(I(7)), vec![L(1), L(0)], 3.0, "".to_string()),
-            Node::new_internal(6, Some(I(8)), vec![L(4), L(3)], 1.0, "".to_string()),
-            Node::new_internal(7, Some(I(8)), vec![I(5), L(2)], 1.0, "".to_string()),
-            Node::new_internal(8, None, vec![I(7), I(6)], 0.0, "".to_string()),
+            Node::new_internal(5, Some(I(7)), vec![L(1), L(0)], 3.0, gen_id(&5)),
+            Node::new_internal(6, Some(I(8)), vec![L(4), L(3)], 1.0, gen_id(&6)),
+            Node::new_internal(7, Some(I(8)), vec![I(5), L(2)], 1.0, gen_id(&7)),
+            Node::new_internal(8, None, vec![I(7), I(6)], 0.0, gen_id(&8)),
         ];
         assert_eq!(nj_tree.root, I(8));
         assert_eq!(nj_tree.nodes, nodes);
@@ -514,9 +518,9 @@ mod tests {
             Node::new_leaf(1, Some(I(4)), 3.0, "B1".to_string()),
             Node::new_leaf(2, Some(I(5)), 2.0, "C2".to_string()),
             Node::new_leaf(3, Some(I(5)), 7.0, "D3".to_string()),
-            Node::new_internal(4, Some(I(6)), vec![L(0), L(1)], 1.0, "".to_string()),
-            Node::new_internal(5, Some(I(6)), vec![L(3), L(2)], 1.0, "".to_string()),
-            Node::new_internal(6, None, vec![I(4), I(5)], 0.0, "".to_string()),
+            Node::new_internal(4, Some(I(6)), vec![L(0), L(1)], 1.0, gen_id(&4)),
+            Node::new_internal(5, Some(I(6)), vec![L(3), L(2)], 1.0, gen_id(&5)),
+            Node::new_internal(6, None, vec![I(4), I(5)], 0.0, gen_id(&6)),
         ];
 
         assert_eq!(nj_tree.root, I(6));
@@ -671,7 +675,11 @@ mod tests {
                 17.0, 14.0, 11.0, 12.0, 10.0, 13.0, 8.0, 0.0;
             ],
         };
-        let sequences = Sequences::new((1..=8).map(|i| record!(&i.to_string(), b"")).collect());
+        let sequences = Sequences::new(
+            (1..=8)
+                .map(|i| record!(format!("s{}", i).as_str(), b""))
+                .collect(),
+        );
 
         // FakeRng will return values that will select the same pairs as in the original paper
         let mut rng = RandomGenerator::from_rng(FakeRng::from_f64_values(vec![
@@ -681,7 +689,7 @@ mod tests {
             .build_from_distances(nj_distances, &sequences, &mut rng)
             .unwrap();
         let correct_tree =
-            tree!("((8:6,7:2):0.5,((5:1,6:4):2,(4:3,(3:1,(1:5,2:2):2):1):2):0.5):0.0;");
+            tree!("((s8:6,s7:2):0.5,((s5:1,s6:4):2,(s4:3,(s3:1,(s1:5,s2:2):2):1):2):0.5):0.0;");
         assert_eq!(nj_tree.length, correct_tree.length);
         for leaf in nj_tree.leaves() {
             assert_eq!(leaf.blen, correct_tree.by_id(&leaf.id).blen);

phylo/src/tree/tests.rs

@@ -213,10 +213,10 @@ fn newick_ladder_big_correct() {
 fn newick_complex_tree_correct() {
     // tree from file samplefraction_0.99_taxa_16_treeheight_0.8_tree1_leaves.nwk
     let trees = from_newick(
-            "(((15:0.0334274,4:0.0334274):0.38581,7:0.419237):0.380763,(((6:0.0973428,14:0.0973428):0.0773821,\
-            (1:0.000738004,3:0.000738004):0.173987):0.548192,(((13:0.0799156,16:0.0799156):0.0667553,(5:0.123516,\
-                10:0.123516):0.0231551):0.0716431,((8:0.0571164,2:0.0571164):0.0539283,(12:0.0631742,(11:0.00312848,\
-                    9:0.00312848):0.0600458):0.0478705):0.107269):0.504603):0.0770827);
+            "(((s15:0.0334274,s4:0.0334274):0.38581,s7:0.419237):0.380763,(((s6:0.0973428,s14:0.0973428):0.0773821,\
+            (s1:0.000738004,s3:0.000738004):0.173987):0.548192,(((s13:0.0799156,s16:0.0799156):0.0667553,(s5:0.123516,\
+                s10:0.123516):0.0231551):0.0716431,((s8:0.0571164,s2:0.0571164):0.0539283,(s12:0.0631742,(s11:0.00312848,\
+                    s9:0.00312848):0.0600458):0.0478705):0.107269):0.504603):0.0770827);
             ",
         )
         .unwrap();
@@ -719,12 +719,12 @@ fn partitions() {
 #[test]
 fn rf_distance_web_example() {
     // Examples from https://cs.hmc.edu/~hadas/mitcompbio/treedistance.html
-    let tree1 = tree!("(0, (1, (2, (3, 4))));");
-    let tree2 = tree!("(0, (1, (3, (2, 4))));");
+    let tree1 = tree!("(s0, (s1, (s2, (s3, s4))));");
+    let tree2 = tree!("(s0, (s1, (s3, (s2, s4))));");
     assert_eq!(tree1.robinson_foulds(&tree2), 2);
 
-    let tree1 = tree!("(0, ((1, (2, 3)), (7, (6, (4, 5)))));");
-    let tree2 = tree!("(0, ((2, (1, 3)), (6, (4, (5, 7)))));");
+    let tree1 = tree!("(s0, ((s1, (s2, s3)), (s7, (s6, (s4, s5)))));");
+    let tree2 = tree!("(s0, ((s2, (s1, s3)), (s6, (s4, (s5, s7)))));");
     assert_eq!(tree1.robinson_foulds(&tree2), 6);
 }