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added test for edge case
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@mmolari
mmolari committed Oct 23, 2024
1 parent b667141 commit 5942c58
Showing 1 changed file with 184 additions and 0 deletions.
184 changes: 184 additions & 0 deletions packages/pangraph/src/circularize/merge_blocks.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -394,6 +394,41 @@ mod tests {
Pangraph { paths, blocks, nodes }
}

fn graph_c() -> Pangraph {
// (0|32) (32|61) (61|0)
// p1) (b1+|n1) -> (b2+|n4) -> (b3+|n7) l=80
// (10|41) (41|72) (72|10)
// p2) (b1+|n2) -> (b2+|n5) -> (b3+|n8) l=83
// (5|40) (40|5)
// p3) (b2-|n6) -> (b1-|n3) l=67

#[rustfmt::skip]
let paths = btreemap! {
PathId(1) => PangraphPath::new(Some(PathId(1)), [1, 4, 7].into_iter().map(NodeId).collect_vec(), 80, true, None),
PathId(2) => PangraphPath::new(Some(PathId(2)), [2, 5, 8].into_iter().map(NodeId).collect_vec(), 83, true, None),
PathId(3) => PangraphPath::new(Some(PathId(3)), [6, 3].into_iter().map(NodeId).collect_vec(), 67, true, None),
};

let blocks = btreemap! {
BlockId(1) => block_1(),
BlockId(2) => block_2(),
BlockId(3) => block_3(),
};

let nodes = btreemap! {
NodeId(1) => PangraphNode::new(Some(NodeId(1)), BlockId(1), PathId(1), Forward, (0, 32)),
NodeId(2) => PangraphNode::new(Some(NodeId(2)), BlockId(1), PathId(2), Forward, (10, 41)),
NodeId(3) => PangraphNode::new(Some(NodeId(3)), BlockId(1), PathId(3), Reverse, (40, 5 )),
NodeId(4) => PangraphNode::new(Some(NodeId(4)), BlockId(2), PathId(1), Forward, (32, 61)),
NodeId(5) => PangraphNode::new(Some(NodeId(5)), BlockId(2), PathId(2), Forward, (41, 72)),
NodeId(6) => PangraphNode::new(Some(NodeId(6)), BlockId(2), PathId(3), Reverse, (5, 40)),
NodeId(7) => PangraphNode::new(Some(NodeId(7)), BlockId(3), PathId(1), Forward, (61, 0 )),
NodeId(8) => PangraphNode::new(Some(NodeId(8)), BlockId(3), PathId(2), Forward, (72, 10)),
};

Pangraph { paths, blocks, nodes }
}

#[test]
fn test_find_node_pairings_a() {
let n1 = SimpleNode::new(BlockId(1), Reverse);
Expand Down Expand Up @@ -436,6 +471,27 @@ mod tests {
);
}

#[test]
fn test_find_node_pairings_c() {
let n1 = SimpleNode::new(BlockId(1), Forward);
let n2 = SimpleNode::new(BlockId(2), Forward);
let edge = Edge { n1, n2 };

let (pairings, new_nodes) = find_node_pairings(&graph_c(), &edge);

assert_eq!(
pairings,
btreemap! {
NodeId(1) => NodeId(4),
NodeId(2) => NodeId(5),
NodeId(3) => NodeId(6),
NodeId(4) => NodeId(1),
NodeId(5) => NodeId(2),
NodeId(6) => NodeId(3),
}
);
}

#[test]
fn test_reverse_complement_1() {
assert_eq!(block_1_revcomp(), block_1().reverse_complement().unwrap());
Expand Down Expand Up @@ -468,6 +524,17 @@ mod tests {
}
}

fn expected_new_nodes_c() -> BTreeMap<NodeId, PangraphNode> {
btreemap! {
NodeId(1) => PangraphNode::new(None, BlockId(1), PathId(1), Forward, (0 , 61)),
NodeId(2) => PangraphNode::new(None, BlockId(1), PathId(2), Forward, (10, 72)),
NodeId(3) => PangraphNode::new(None, BlockId(1), PathId(3), Reverse, (5, 5)),
NodeId(4) => PangraphNode::new(None, BlockId(1), PathId(1), Forward, (0 , 61)),
NodeId(5) => PangraphNode::new(None, BlockId(1), PathId(2), Forward, (10, 72)),
NodeId(6) => PangraphNode::new(None, BlockId(1), PathId(3), Reverse, (5, 5)),
}
}

fn expected_new_node_ids_a() -> BTreeMap<NodeId, NodeId> {
expected_new_nodes_a().iter().map(|(&k, v)| (k, v.id())).collect()
}
Expand All @@ -476,6 +543,10 @@ mod tests {
expected_new_nodes_b().iter().map(|(&k, v)| (k, v.id())).collect()
}

fn expected_new_node_ids_c() -> BTreeMap<NodeId, NodeId> {
expected_new_nodes_c().iter().map(|(&k, v)| (k, v.id())).collect()
}

fn expected_concat_a() -> PangraphBlock {
// 0 1 2 3 4 5 6
// 012345678901234567890123456789012345678901234567890123456789012
Expand Down Expand Up @@ -518,6 +589,27 @@ mod tests {
)
}

fn expected_concat_c() -> PangraphBlock {
// 0 1 2 3 4 5 6
// 01234567890123456789012345678901 2345678901234567890123456789012
// cons: ACTATATTACGGCGATCGATCGATTACTCGCT GATCTTAGGATCATCCCTATCATAGGAGTCG
// n1: ...G............................ .........................xx....
// n2: .......|.....xxx................ ...T...........................
// n3: ................................||xx.............................
let new_ids = expected_new_node_ids_a();
let aln = btreemap! {
new_ids[&NodeId(1)] => Edit::new(vec![], vec![Del::new(57, 2)], vec![Sub::new(3 , 'G')]),
new_ids[&NodeId(2)] => Edit::new(vec![Ins::new(7, "AA")], vec![Del::new(13, 3)], vec![Sub::new(35, 'T')]),
new_ids[&NodeId(3)] => Edit::new(vec![Ins::new(32, "CCCTTT")], vec![Del::new(32, 2)], vec![] ),
};

PangraphBlock::new(
BlockId(1),
"ACTATATTACGGCGATCGATCGATTACTCGCTGATCTTAGGATCATCCCTATCATAGGAGTCG",
aln,
)
}

#[test]
fn test_concatenate_blocks_a() {
let n1 = SimpleNode::new(BlockId(1), Forward);
Expand Down Expand Up @@ -556,6 +648,19 @@ mod tests {
assert_eq!(block, expected_concat_b());
}

#[test]
fn test_concatenate_blocks_c() {
let n1 = SimpleNode::new(BlockId(1), Forward);
let n2 = SimpleNode::new(BlockId(2), Forward);
let edge = Edge::new(n1, n2);

let (pairings, new_nodes) = find_node_pairings(&graph_c(), &edge);

let new_nodes_ids = expected_new_node_ids_c();
let block = concatenate_alignments(&block_1(), &block_2(), &pairings, &new_nodes_ids, BlockId(1));
assert_eq!(block, expected_concat_c());
}

fn expected_graph_a() -> Pangraph {
// (0|-----------|61) (61|0)
// p1) (b1+|-----------|n1) -> (b3+|n7) l=80
Expand Down Expand Up @@ -628,6 +733,42 @@ mod tests {
Pangraph { paths, blocks, nodes }
}

fn expected_graph_c() -> Pangraph {
// (0|-----------|61) (61|0)
// p1) (b1+|-----------|n1) -> (b3+|n7) l=80
// (10|-----------|72) (72|10)
// p2) (b1+|-----------|n2) -> (b3+|n8) l=83
// (40|-----------|40)
// p3) (b1-|-----------|n3) l=67

let new_ids = expected_new_node_ids_c();

let blocks = btreemap! {
BlockId(1) => expected_concat_c(),
BlockId(3) => PangraphBlock::new(BlockId(3), "CTATTACTAGGGGGACCACTA", btreemap! {
NodeId(7) => Edit::new(vec![], vec![Del::new(15, 2)], vec![] ),
NodeId(8) => Edit::new(vec![], vec![], vec![Sub::new(3, 'C')]),
})
};

let nodes = btreemap! {
new_ids[&NodeId(1)] => PangraphNode::new(None, BlockId(1), PathId(1), Forward, (0 , 61)),
new_ids[&NodeId(2)] => PangraphNode::new(None, BlockId(1), PathId(2), Forward, (10, 72)),
new_ids[&NodeId(3)] => PangraphNode::new(None, BlockId(1), PathId(3), Reverse, (5, 5)),
NodeId(7) => PangraphNode::new(Some(NodeId(7)), BlockId(3), PathId(1), Forward, (61, 0 )),
NodeId(8) => PangraphNode::new(Some(NodeId(8)), BlockId(3), PathId(2), Forward, (72, 10)),
};

#[rustfmt::skip]
let paths = btreemap! {
PathId(1) => PangraphPath::new(Some(PathId(1)), [new_ids[&NodeId(1)], NodeId(7)], 80, true, None),
PathId(2) => PangraphPath::new(Some(PathId(2)), [new_ids[&NodeId(2)], NodeId(8)], 83, true, None),
PathId(3) => PangraphPath::new(Some(PathId(3)), [new_ids[&NodeId(3)]], 67, true, None)
};

Pangraph { paths, blocks, nodes }
}

#[test]
fn test_update_paths_a() {
let n1 = SimpleNode::new(BlockId(1), Forward);
Expand All @@ -650,6 +791,17 @@ mod tests {
assert_eq!(g.paths, expected_graph_b().paths);
}

#[test]
fn test_update_paths_c() {
let n1 = SimpleNode::new(BlockId(1), Forward);
let n2 = SimpleNode::new(BlockId(2), Forward);
let edge = Edge::new(n1, n2);
let mut g = graph_c();
let (pairings, new_nodes) = find_node_pairings(&g, &edge);
graph_merging_update_paths(&mut g, &new_nodes, BlockId(1));
assert_eq!(g.paths, expected_graph_c().paths);
}

#[test]
fn test_update_nodes_a() {
let n1 = SimpleNode::new(BlockId(1), Forward);
Expand All @@ -672,6 +824,17 @@ mod tests {
assert_eq!(g.nodes, expected_graph_b().nodes);
}

#[test]
fn test_update_nodes_c() {
let n1 = SimpleNode::new(BlockId(1), Forward);
let n2 = SimpleNode::new(BlockId(2), Forward);
let edge = Edge::new(n1, n2);
let mut g = graph_c();
let (pairings, new_nodes) = find_node_pairings(&g, &edge);
graph_merging_update_nodes(&mut g, &new_nodes, BlockId(1));
assert_eq!(g.nodes, expected_graph_c().nodes);
}

#[test]
fn test_merge_blocks_a() {
let n1 = SimpleNode::new(BlockId(1), Forward);
Expand All @@ -696,6 +859,18 @@ mod tests {
assert_eq!(g.paths, expected_graph_b().paths);
}

#[test]
fn test_merge_blocks_c() {
let n1 = SimpleNode::new(BlockId(1), Forward);
let n2 = SimpleNode::new(BlockId(2), Forward);
let edge = Edge::new(n1, n2);
let mut g = graph_c();
merge_blocks(&mut g, edge).unwrap();
assert_eq!(g.nodes, expected_graph_c().nodes);
assert_eq!(g.blocks, expected_graph_c().blocks);
assert_eq!(g.paths, expected_graph_c().paths);
}

#[test]
fn test_remove_transitive_edges_a() {
let mut g = graph_a();
Expand All @@ -713,4 +888,13 @@ mod tests {
assert_eq!(g.blocks, expected_graph_b().blocks);
assert_eq!(g.paths, expected_graph_b().paths);
}

#[test]
fn test_remove_transitive_edges_c() {
let mut g = graph_c();
remove_transitive_edges(&mut g).unwrap();
assert_eq!(g.nodes, expected_graph_c().nodes);
assert_eq!(g.blocks, expected_graph_c().blocks);
assert_eq!(g.paths, expected_graph_c().paths);
}
}

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