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Generate mappings of common ranges from one path to another #73

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merged 6 commits into from
Oct 30, 2024
+2,149 −47
Merged

Generate mappings of common ranges from one path to another #73

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6116f13
Map ranges from one path to another
dkhofer Oct 16, 2024
f4854d2
Fix comment indentation
dkhofer Oct 16, 2024
e0cf111
Map annotations across paths, use self more
dkhofer Oct 16, 2024
9b9c911
Annotation tests
dkhofer Oct 16, 2024
9e1cb1b
Some comments and new test
dkhofer Oct 17, 2024
063364f
Fixes after rebase; address comment
dkhofer Oct 30, 2024
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4 changes: 2 additions & 2 deletions src/exports/gfa.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -361,7 +361,7 @@ mod tests {

let paths = Path::get_paths_for_collection(&conn, "test collection 2");
assert_eq!(paths.len(), 1);
assert_eq!(Path::sequence(&conn, paths[0].clone()), "AAAATTTTGGGGCCCC");
assert_eq!(paths[0].sequence(&conn), "AAAATTTTGGGGCCCC");
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}

#[test]
Expand Down Expand Up @@ -477,7 +477,7 @@ mod tests {
chromosome_index: 1,
phased: 0,
};
let tree = Path::intervaltree_for(&conn, &path);
let tree = path.intervaltree(&conn);
BlockGroup::insert_change(&conn, &change, &tree);

let edges = BlockGroupEdge::edges_for_block_group(&conn, block_group_id);
Expand Down
4 changes: 2 additions & 2 deletions src/imports/fasta.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -151,7 +151,7 @@ mod tests {

let path = Path::get(&conn, 1);
assert_eq!(
Path::sequence(&conn, path),
path.sequence(&conn),
"ATCGATCGATCGATCGATCGGGAACACACAGAGA".to_string()
);
}
Expand Down Expand Up @@ -180,7 +180,7 @@ mod tests {

let path = Path::get(&conn, 1);
assert_eq!(
Path::sequence(&conn, path),
path.sequence(&conn),
"ATCGATCGATCGATCGATCGGGAACACACAGAGA".to_string()
);
}
Expand Down
10 changes: 5 additions & 5 deletions src/imports/gfa.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -243,7 +243,7 @@ mod tests {
)[0]
.clone();

let result = Path::sequence(conn, path);
let result = path.sequence(conn);
assert_eq!(result, "ATCGATCGATCGATCGATCGGGAACACACAGAGA");

let node_count = Node::query(conn, "select * from nodes", vec![]).len() as i64;
Expand Down Expand Up @@ -288,7 +288,7 @@ mod tests {
)[0]
.clone();

let result = Path::sequence(conn, path);
let result = path.sequence(conn);
assert_eq!(result, "ACCTACAAATTCAAAC");

let node_count = Node::query(conn, "select * from nodes", vec![]).len() as i64;
Expand All @@ -314,7 +314,7 @@ mod tests {
)[0]
.clone();

let result = Path::sequence(conn, path);
let result = path.sequence(conn);
assert_eq!(result, "TATGCCAGCTGCGAATA");

let node_count = Node::query(conn, "select * from nodes", vec![]).len() as i64;
Expand Down Expand Up @@ -343,7 +343,7 @@ mod tests {
)[0]
.clone();

let result = Path::sequence(conn, path);
let result = path.sequence(conn);
let big_part = "TGCTAGCTACTAGTGAAAGAGGAGAAATACTAGATGGCTTCCTCCGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATGGAAGGTTCCGTTAACGGTCACGAGTTCGAAATCGAAGGTGAAGGTGAAGGTCGTCCGTACGAAGGTACCCAGACCGCTAAACTGAAAGTTACCAAAGGTGGTCCGCTGCCGTTCGCTTGGGACATCCTGTCCCCGCAGTTCCAGTACGGTTCCAAAGCTTACGTTAAACACCCGGCTGACATCCCGGACTACCTGAAACTGTCCTTCCCGGAAGGTTTCAAATGGGAACGTGTTATGAACTTCGAAGACGGTGGTGTTGTTACCGTTACCCAGGACTCCTCCCTGCAAGACGGTGAGTTCATCTACAAAGTTAAACTGCGTGGTACCAACTTCCCGTCCGACGGTCCGGTTATGCAGAAAAAAACCATGGGTTGGGAAGCTTCCACCGAACGTATGTACCCGGAAGACGGTGCTCTGAAAGGTGAAATCAAAATGCGTCTGAAACTGAAAGACGGTGGTCACTACGACGCTGAAGTTAAAACCACCTACATGGCTAAAAAACCGGTTCAGCTGCCGGGTGCTTACAAAACCGACATCAAACTGGACATCACCTCCCACAACGAAGACTACACCATCGTTGAACAGTACGAACGTGCTGAAGGTCGTCACTCCACCGGTGCTTAATAACGCTGATAGTGCTAGTGTAGATCGCTACTAGAGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCTACTAGAGTCACACTGGCTCACCTTCGGGTGGGCCTTTCTGCGTTTATATACTAGAAGCGGCCGCTGCAGGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACATTTCCCCGAAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGACATTAACCTATAAAAATAGGCGTATCACGAGGCAGAATTTCAGATAAAAAAAATCCTTAGCTTTCGCTAAGGATGATTTCTGGAATTCGCGGCCGCATCTAGAG";
let expected_sequence_parts = vec![
"T",
Expand Down Expand Up @@ -446,7 +446,7 @@ mod tests {
)[0]
.clone();

let result = Path::sequence(conn, path);
let result = path.sequence(conn);
assert_eq!(result, "AA");

let all_sequences = BlockGroup::get_all_sequences(conn, block_group_id);
Expand Down
1 change: 1 addition & 0 deletions src/lib.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@ pub mod imports;
pub mod migrations;
pub mod models;
pub mod operation_management;
pub mod range;
pub mod test_helpers;
pub mod updates;

Expand Down
44 changes: 22 additions & 22 deletions src/models/block_group.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -76,7 +76,7 @@ impl PathCache<'_> {
.clone();

path_cache.cache.insert(path_key, new_path.clone());
let tree = Path::intervaltree_for(path_cache.conn, &new_path);
let tree = new_path.intervaltree(path_cache.conn);
path_cache.intervaltree_cache.insert(new_path.clone(), tree);
new_path
}
Expand Down Expand Up @@ -721,7 +721,7 @@ mod tests {
chromosome_index: 1,
phased: 0,
};
let tree = Path::intervaltree_for(&conn, &path);
let tree = path.intervaltree(&conn);
BlockGroup::insert_change(&conn, &change, &tree);

let all_sequences = BlockGroup::get_all_sequences(&conn, block_group_id);
Expand Down Expand Up @@ -760,7 +760,7 @@ mod tests {
phased: 0,
};
// take out an entire block.
let tree = Path::intervaltree_for(&conn, &path);
let tree = path.intervaltree(&conn);
BlockGroup::insert_change(&conn, &change, &tree);
let all_sequences = BlockGroup::get_all_sequences(&conn, block_group_id);
assert_eq!(
Expand Down Expand Up @@ -803,7 +803,7 @@ mod tests {
chromosome_index: 1,
phased: 0,
};
let tree = Path::intervaltree_for(&conn, &path);
let tree = path.intervaltree(&conn);
BlockGroup::insert_change(&conn, &change, &tree);

let all_sequences = BlockGroup::get_all_sequences(&conn, block_group_id);
Expand Down Expand Up @@ -845,7 +845,7 @@ mod tests {
chromosome_index: 1,
phased: 0,
};
let tree = Path::intervaltree_for(&conn, &path);
let tree = path.intervaltree(&conn);
BlockGroup::insert_change(&conn, &change, &tree);

let all_sequences = BlockGroup::get_all_sequences(&conn, block_group_id);
Expand Down Expand Up @@ -887,7 +887,7 @@ mod tests {
chromosome_index: 1,
phased: 0,
};
let tree = Path::intervaltree_for(&conn, &path);
let tree = path.intervaltree(&conn);
BlockGroup::insert_change(&conn, &change, &tree);

let all_sequences = BlockGroup::get_all_sequences(&conn, block_group_id);
Expand Down Expand Up @@ -929,7 +929,7 @@ mod tests {
chromosome_index: 1,
phased: 0,
};
let tree = Path::intervaltree_for(&conn, &path);
let tree = path.intervaltree(&conn);
BlockGroup::insert_change(&conn, &change, &tree);

let all_sequences = BlockGroup::get_all_sequences(&conn, block_group_id);
Expand Down Expand Up @@ -971,7 +971,7 @@ mod tests {
chromosome_index: 1,
phased: 0,
};
let tree = Path::intervaltree_for(&conn, &path);
let tree = path.intervaltree(&conn);
BlockGroup::insert_change(&conn, &change, &tree);

let all_sequences = BlockGroup::get_all_sequences(&conn, block_group_id);
Expand Down Expand Up @@ -1013,7 +1013,7 @@ mod tests {
chromosome_index: 1,
phased: 0,
};
let tree = Path::intervaltree_for(&conn, &path);
let tree = path.intervaltree(&conn);
BlockGroup::insert_change(&conn, &change, &tree);

let all_sequences = BlockGroup::get_all_sequences(&conn, block_group_id);
Expand Down Expand Up @@ -1055,7 +1055,7 @@ mod tests {
chromosome_index: 1,
phased: 0,
};
let tree = Path::intervaltree_for(&conn, &path);
let tree = path.intervaltree(&conn);
BlockGroup::insert_change(&conn, &change, &tree);

let all_sequences = BlockGroup::get_all_sequences(&conn, block_group_id);
Expand Down Expand Up @@ -1097,7 +1097,7 @@ mod tests {
chromosome_index: 1,
phased: 0,
};
let tree = Path::intervaltree_for(&conn, &path);
let tree = path.intervaltree(&conn);
BlockGroup::insert_change(&conn, &change, &tree);

let all_sequences = BlockGroup::get_all_sequences(&conn, block_group_id);
Expand Down Expand Up @@ -1142,7 +1142,7 @@ mod tests {
};

// take out an entire block.
let tree = Path::intervaltree_for(&conn, &path);
let tree = path.intervaltree(&conn);
BlockGroup::insert_change(&conn, &change, &tree);
let all_sequences = BlockGroup::get_all_sequences(&conn, block_group_id);
assert_eq!(
Expand Down Expand Up @@ -1183,7 +1183,7 @@ mod tests {
chromosome_index: 1,
phased: 0,
};
let tree = Path::intervaltree_for(&conn, &path);
let tree = path.intervaltree(&conn);
BlockGroup::insert_change(&conn, &change, &tree);

let all_sequences = BlockGroup::get_all_sequences(&conn, block_group_id);
Expand All @@ -1195,7 +1195,7 @@ mod tests {
])
);

let tree = Path::intervaltree_for(&conn, &path);
let tree = path.intervaltree(&conn);
BlockGroup::insert_change(&conn, &change, &tree);

let all_sequences = BlockGroup::get_all_sequences(&conn, block_group_id);
Expand Down Expand Up @@ -1237,7 +1237,7 @@ mod tests {
chromosome_index: 1,
phased: 0,
};
let tree = Path::intervaltree_for(&conn, &path);
let tree = path.intervaltree(&conn);
BlockGroup::insert_change(&conn, &change, &tree);

let all_sequences = BlockGroup::get_all_sequences(&conn, block_group_id);
Expand Down Expand Up @@ -1280,7 +1280,7 @@ mod tests {
chromosome_index: 1,
phased: 0,
};
let tree = Path::intervaltree_for(&conn, &path);
let tree = path.intervaltree(&conn);
BlockGroup::insert_change(&conn, &change, &tree);

let all_sequences = BlockGroup::get_all_sequences(&conn, block_group_id);
Expand Down Expand Up @@ -1322,7 +1322,7 @@ mod tests {
chromosome_index: 1,
phased: 0,
};
let tree = Path::intervaltree_for(&conn, &path);
let tree = path.intervaltree(&conn);
BlockGroup::insert_change(&conn, &change, &tree);

let all_sequences = BlockGroup::get_all_sequences(&conn, block_group_id);
Expand Down Expand Up @@ -1364,7 +1364,7 @@ mod tests {
chromosome_index: 1,
phased: 0,
};
let tree = Path::intervaltree_for(&conn, &path);
let tree = path.intervaltree(&conn);
BlockGroup::insert_change(&conn, &change, &tree);

let all_sequences = BlockGroup::get_all_sequences(&conn, block_group_id);
Expand Down Expand Up @@ -1406,7 +1406,7 @@ mod tests {
chromosome_index: 1,
phased: 0,
};
let tree = Path::intervaltree_for(&conn, &path);
let tree = path.intervaltree(&conn);
BlockGroup::insert_change(&conn, &change, &tree);

let all_sequences = BlockGroup::get_all_sequences(&conn, block_group_id);
Expand Down Expand Up @@ -1448,7 +1448,7 @@ mod tests {
chromosome_index: 1,
phased: 0,
};
let tree = Path::intervaltree_for(&conn, &path);
let tree = path.intervaltree(&conn);
BlockGroup::insert_change(&conn, &change, &tree);

let all_sequences = BlockGroup::get_all_sequences(&conn, block_group_id);
Expand Down Expand Up @@ -1490,7 +1490,7 @@ mod tests {
chromosome_index: 1,
phased: 0,
};
let tree = Path::intervaltree_for(&conn, &path);
let tree = path.intervaltree(&conn);
BlockGroup::insert_change(&conn, &change, &tree);

let all_sequences = BlockGroup::get_all_sequences(&conn, block_group_id);
Expand Down Expand Up @@ -1532,7 +1532,7 @@ mod tests {
chromosome_index: 1,
phased: 0,
};
let tree = Path::intervaltree_for(&conn, &path);
let tree = path.intervaltree(&conn);
BlockGroup::insert_change(&conn, &change, &tree);

let all_sequences = BlockGroup::get_all_sequences(&conn, block_group_id);
Expand Down
2 changes: 1 addition & 1 deletion src/models/edge.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -815,7 +815,7 @@ mod tests {
chromosome_index: 1,
phased: 0,
};
let tree = Path::intervaltree_for(&conn, &path);
let tree = path.intervaltree(&conn);
BlockGroup::insert_change(&conn, &change, &tree);
let mut edges = BlockGroupEdge::edges_for_block_group(&conn, block_group_id);

Expand Down
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