feat: add mode of inheritance from HPO (#493)

protos/varfish/v1/seqvars/output.proto

@@ -166,12 +166,32 @@ message GeneRelatedConsequences {
   repeated varfish.v1.seqvars.query.Consequence consequences = 3;
 }
 
+// Enumerations with modes of inheritance from HPO.
+enum ModeOfInheritance {
+  // Unspecified mode of inheritance.
+  MODE_OF_INHERITANCE_UNSPECIFIED = 0;
+  // Autosomal dominant inheritance (HP:0000006).
+  MODE_OF_INHERITANCE_AUTOSOMAL_DOMINANT = 1;
+  // Autosomal recessive inheritance (HP:0000007).
+  MODE_OF_INHERITANCE_AUTOSOMAL_RECESSIVE = 2;
+  // X-linked dominant inheritance (HP:0001419).
+  MODE_OF_INHERITANCE_X_LINKED_DOMINANT = 3;
+  // X-linked recessive inheritance (HP:0001423).
+  MODE_OF_INHERITANCE_X_LINKED_RECESSIVE = 4;
+  // Y-linked inheritance (HP:0001450).
+  MODE_OF_INHERITANCE_Y_LINKED = 5;
+  // Mitochondrial inheritance (HP:0001427).
+  MODE_OF_INHERITANCE_MITOCHONDRIAL = 6;
+}
+
 // Phenotype-related information, if any.
 message GeneRelatedPhenotypes {
   // ACMG supplementary finding list.
   bool is_acmg_sf = 1;
   // Whether is a known disease gene.
   bool is_disease_gene = 2;
+  // Linked modes of inheritance.
+  repeated ModeOfInheritance mode_of_inheritances = 3;
 }
 
 // Gene-wise constraints.

src/seqvars/query/annonars.rs

@@ -6,11 +6,14 @@ use crate::{common::GenomeRelease, seqvars::ingest::path_component};
 
 use prost::Message as _;
 
-use super::schema::data::VariantRecord;
+use super::{
+    hpo::{load_hgnc_to_inheritance_map, HgncToMoiMap},
+    schema::data::VariantRecord,
+};
 
 /// Bundle the types needed for databases.
 pub struct AnnonarsDbs {
-    /// annonaars gene RocksDB.
+    /// annonars gene RocksDB.
     pub genes_db: Arc<rocksdb::DBWithThreadMode<rocksdb::MultiThreaded>>,
     /// ClinVar database as annonars RocksDB.
     pub clinvar_db: Arc<rocksdb::DBWithThreadMode<rocksdb::MultiThreaded>>,
@@ -124,6 +127,8 @@ impl AnnonarsDbs {
 pub struct Annotator {
     /// Annonars database bundles.
     pub annonars_dbs: AnnonarsDbs,
+    /// Mapping from HGNC gene ID to modes of inheritance; from `hpo` directory.
+    pub hgnc_to_moi: HgncToMoiMap,
 }
 
 impl Annotator {
@@ -143,7 +148,18 @@ impl Annotator {
                 e
             )
         })?;
-        Ok(Self { annonars_dbs })
+        let hgnc_to_moi =
+            load_hgnc_to_inheritance_map(&path.as_ref().join("hpo")).map_err(|e| {
+                anyhow::anyhow!(
+                    "problem loading HGNC to mode of inheritance map at {}: {}",
+                    path.as_ref().join("hpo").display(),
+                    e
+                )
+            })?;
+        Ok(Self {
+            annonars_dbs,
+            hgnc_to_moi,
+        })
     }
 
     /// Query `genes` database for a given HGNC ID.

src/seqvars/query/hpo.rs

@@ -0,0 +1,315 @@
+//! Code for accessing HPO-related information.
+
+use crate::pbs::varfish::v1::seqvars::output as pbs_output;
+
+/// Enumeration for modes of inheritance.
+#[derive(
+    serde::Serialize,
+    serde::Deserialize,
+    enum_map::Enum,
+    PartialEq,
+    Eq,
+    PartialOrd,
+    Ord,
+    Hash,
+    Clone,
+    Copy,
+    Debug,
+    strum::EnumString,
+    strum::Display,
+)]
+pub enum ModeOfInheritance {
+    /// Autosomal dominant inheritance (HP:0000006).
+    AutosomalDominant,
+    /// Autosomal recessive inheritance (HP:0000007).
+    AutosomalRecessive,
+    /// X-linked dominant inheritance (HP:0001419).
+    XLinkedDominant,
+    /// X-linked recessive inheritance (HP:0001423).
+    XLinkedRecessive,
+    /// Y-linked inheritance (HP:0001450).
+    YLinked,
+    /// Mitochondrial inheritance (HP:0001427).
+    Mitochondrial,
+}
+
+impl ModeOfInheritance {
+    /// Allow parsing of `ModeOfInheritance` from HPO ID.
+    pub fn from_hpo_id(hpo_id: &str) -> Option<Self> {
+        match hpo_id {
+            "HP:0000006" | "HP:0012275" => Some(Self::AutosomalDominant),
+            "HP:0000007" => Some(Self::AutosomalRecessive),
+            "HP:0001419" => Some(Self::XLinkedDominant),
+            "HP:0001423" => Some(Self::XLinkedRecessive),
+            "HP:0001450" => Some(Self::YLinked),
+            "HP:0001427" => Some(Self::Mitochondrial),
+            _ => None,
+        }
+    }
+}
+
+impl From<ModeOfInheritance> for pbs_output::ModeOfInheritance {
+    fn from(val: ModeOfInheritance) -> Self {
+        match val {
+            ModeOfInheritance::AutosomalDominant => {
+                pbs_output::ModeOfInheritance::AutosomalDominant
+            }
+            ModeOfInheritance::AutosomalRecessive => {
+                pbs_output::ModeOfInheritance::AutosomalRecessive
+            }
+            ModeOfInheritance::XLinkedDominant => pbs_output::ModeOfInheritance::XLinkedDominant,
+            ModeOfInheritance::XLinkedRecessive => pbs_output::ModeOfInheritance::XLinkedRecessive,
+            ModeOfInheritance::YLinked => pbs_output::ModeOfInheritance::YLinked,
+            ModeOfInheritance::Mitochondrial => pbs_output::ModeOfInheritance::Mitochondrial,
+        }
+    }
+}
+
+pub type HgncToMoiMap = indexmap::IndexMap<String, indexmap::IndexSet<ModeOfInheritance>>;
+
+/// Load the the `phenotype_to_genes.tsv` and `hgnc_xlink.tsv` files from the `hpo`
+/// directory and build a map from HGNC gene ID to set of `ModeOfInheritance`
+/// values.
+pub fn load_hgnc_to_inheritance_map<P: AsRef<std::path::Path>>(
+    path: &P,
+) -> Result<HgncToMoiMap, anyhow::Error> {
+    let phenotypes_to_genes =
+        phenotype_to_genes::load_entries(&path.as_ref().join("phenotype_to_genes.txt"))
+            .map_err(|e| anyhow::anyhow!("error loading phenotype_to_genes.txt: {}", e))?;
+    let ncbi_to_hgnc = hgnc_xlink::load_ncbi_to_hgnc(path.as_ref().join("hgnc_xlink.tsv"))
+        .map_err(|e| anyhow::anyhow!("error loading hgnc_xlink.tsv: {}", e))?;
+
+    let mut result = indexmap::IndexMap::new();
+
+    for ptg_entry in phenotypes_to_genes {
+        if let Some(ncbi_gene_id) = ptg_entry.ncbi_gene_id {
+            if let Some(hgnc_ids) = ncbi_to_hgnc.get(&ncbi_gene_id) {
+                for hgnc_id in hgnc_ids {
+                    if let Some(mode_of_inheritance) =
+                        ModeOfInheritance::from_hpo_id(&ptg_entry.hpo_id)
+                    {
+                        let mode_of_inheritances = result
+                            .entry(hgnc_id.clone())
+                            .or_insert_with(indexmap::IndexSet::new);
+                        mode_of_inheritances.insert_sorted(mode_of_inheritance);
+                    }
+                }
+            }
+        }
+    }
+
+    Ok(result)
+}
+
+/// Code for accessing the `phenotype_to_genes.tsv` file.
+pub(super) mod phenotype_to_genes {
+    /// Data structure for representing an entry of the table.
+    #[derive(Debug, Clone, serde::Serialize, serde::Deserialize)]
+    #[serde_with::skip_serializing_none]
+    pub struct Entry {
+        /// Entrez gene ID.
+        #[serde(alias = "entrez_id")]
+        pub ncbi_gene_id: Option<u32>,
+        /// Gene symbol.
+        pub gene_symbol: String,
+        /// HPO ID.
+        pub hpo_id: String,
+        // HPO Name.
+        pub hpo_name: String,
+    }
+
+    /// Read the `phenotype_to_genes.tsv` file using the `csv` crate via serde.
+    ///
+    /// # Errors
+    ///
+    /// In the case that the file could not be read.
+    pub fn load_entries<P: AsRef<std::path::Path>>(path: &P) -> Result<Vec<Entry>, anyhow::Error> {
+        let mut rdr = csv::ReaderBuilder::new()
+            .delimiter(b'\t')
+            .has_headers(true)
+            .from_path(path.as_ref())?;
+        let mut entries = Vec::new();
+        for result in rdr.deserialize() {
+            let entry: Entry = result?;
+            entries.push(entry);
+        }
+        Ok(entries)
+    }
+}
+
+/// Code for accessing the `hgnc_xlink.tsv` file.
+pub(super) mod hgnc_xlink {
+    use std::collections::HashMap;
+
+    /// Data structure for representing an entry of the table.
+    #[derive(Debug, Clone, serde::Serialize, serde::Deserialize)]
+    #[serde_with::skip_serializing_none]
+    pub struct Entry {
+        /// HGNC gene ID.
+        pub hgnc_id: String,
+        /// Ensembl gene ID.
+        pub ensembl_gene_id: Option<String>,
+        /// Entrez gene ID.
+        #[serde(alias = "entrez_id")]
+        pub ncbi_gene_id: Option<u32>,
+        /// Gene symbol.
+        pub gene_symbol: String,
+    }
+
+    /// Read the `hgnc_xlink.tsv` file using the `csv` crate via serde.
+    ///
+    /// # Errors
+    ///
+    /// In the case that the file could not be read.
+    pub fn load_entries<P: AsRef<std::path::Path>>(path: &P) -> Result<Vec<Entry>, anyhow::Error> {
+        let mut rdr = csv::ReaderBuilder::new()
+            .delimiter(b'\t')
+            .has_headers(true)
+            .from_path(path.as_ref())?;
+        let mut entries = Vec::new();
+        for result in rdr.deserialize() {
+            let entry: Entry = result?;
+            entries.push(entry);
+        }
+        Ok(entries)
+    }
+
+    /// Read the `hgnc_xlink.tsv` into a map from NCBI gene ID to HGNC gene ID.
+    ///
+    /// # Errors
+    ///
+    /// In the case that the file could not be read.
+    pub fn load_ncbi_to_hgnc<P: AsRef<std::path::Path>>(
+        path: P,
+    ) -> Result<HashMap<u32, Vec<String>>, anyhow::Error> {
+        let mut map = HashMap::new();
+        for entry in load_entries(&path)? {
+            if let Some(ncbi_gene_id) = entry.ncbi_gene_id {
+                let hgnc_id = entry.hgnc_id;
+                let entry = map.entry(ncbi_gene_id).or_insert_with(Vec::new);
+                entry.push(hgnc_id);
+            }
+        }
+        Ok(map)
+    }
+}
+
+#[cfg(test)]
+mod test {
+    #[test]
+    pub fn test_mode_of_inheritance_from_hpo_id() {
+        assert_eq!(
+            super::ModeOfInheritance::from_hpo_id("HP:0000006"),
+            Some(super::ModeOfInheritance::AutosomalDominant)
+        );
+        assert_eq!(
+            super::ModeOfInheritance::from_hpo_id("HP:0012275"),
+            Some(super::ModeOfInheritance::AutosomalDominant)
+        );
+        assert_eq!(
+            super::ModeOfInheritance::from_hpo_id("HP:0000007"),
+            Some(super::ModeOfInheritance::AutosomalRecessive)
+        );
+        assert_eq!(
+            super::ModeOfInheritance::from_hpo_id("HP:0001419"),
+            Some(super::ModeOfInheritance::XLinkedDominant)
+        );
+        assert_eq!(
+            super::ModeOfInheritance::from_hpo_id("HP:0001423"),
+            Some(super::ModeOfInheritance::XLinkedRecessive)
+        );
+        assert_eq!(
+            super::ModeOfInheritance::from_hpo_id("HP:0001450"),
+            Some(super::ModeOfInheritance::YLinked)
+        );
+        assert_eq!(
+            super::ModeOfInheritance::from_hpo_id("HP:0001427"),
+            Some(super::ModeOfInheritance::Mitochondrial)
+        );
+
+        assert_eq!(super::ModeOfInheritance::from_hpo_id("HP:0000000"), None);
+    }
+
+    #[test]
+    pub fn test_mode_of_inheritance_into_pbs() {
+        assert_eq!(
+            Into::<super::pbs_output::ModeOfInheritance>::into(
+                super::ModeOfInheritance::AutosomalDominant
+            ),
+            super::pbs_output::ModeOfInheritance::AutosomalDominant
+        );
+        assert_eq!(
+            Into::<super::pbs_output::ModeOfInheritance>::into(
+                super::ModeOfInheritance::AutosomalRecessive
+            ),
+            super::pbs_output::ModeOfInheritance::AutosomalRecessive
+        );
+        assert_eq!(
+            Into::<super::pbs_output::ModeOfInheritance>::into(
+                super::ModeOfInheritance::XLinkedDominant
+            ),
+            super::pbs_output::ModeOfInheritance::XLinkedDominant
+        );
+        assert_eq!(
+            Into::<super::pbs_output::ModeOfInheritance>::into(
+                super::ModeOfInheritance::XLinkedRecessive
+            ),
+            super::pbs_output::ModeOfInheritance::XLinkedRecessive
+        );
+        assert_eq!(
+            Into::<super::pbs_output::ModeOfInheritance>::into(super::ModeOfInheritance::YLinked),
+            super::pbs_output::ModeOfInheritance::YLinked
+        );
+        assert_eq!(
+            Into::<super::pbs_output::ModeOfInheritance>::into(
+                super::ModeOfInheritance::Mitochondrial
+            ),
+            super::pbs_output::ModeOfInheritance::Mitochondrial
+        );
+    }
+
+    #[test]
+    fn load_hgnc_to_inheritance_map() -> Result<(), anyhow::Error> {
+        let path = std::path::Path::new("tests/seqvars/query/db/hpo");
+        let map = super::load_hgnc_to_inheritance_map(&path)?;
+
+        assert_eq!(map.len(), 4599);
+        insta::assert_yaml_snapshot!(&map[0..5]);
+
+        Ok(())
+    }
+
+    #[test]
+    fn test_phenotype_to_genes_load_entries() -> Result<(), anyhow::Error> {
+        let path = std::path::Path::new("tests/seqvars/query/db/hpo/phenotype_to_genes.txt");
+        let entries = super::phenotype_to_genes::load_entries(&path)?;
+
+        assert_eq!(entries.len(), 988720);
+        insta::assert_yaml_snapshot!(&entries[0..5]);
+
+        Ok(())
+    }
+
+    #[test]
+    fn test_hgnc_to_xlink_load_entries() -> Result<(), anyhow::Error> {
+        let path = std::path::Path::new("tests/seqvars/query/db/hpo/hgnc_xlink.tsv");
+        let map = super::hgnc_xlink::load_entries(&path)?;
+
+        assert_eq!(map.len(), 43839);
+        insta::assert_yaml_snapshot!(&map[0..5]);
+
+        Ok(())
+    }
+
+    #[test]
+    fn test_load_ncbi_to_hgnc() -> Result<(), anyhow::Error> {
+        let path = std::path::Path::new("tests/seqvars/query/db/hpo/hgnc_xlink.tsv");
+        let map = super::hgnc_xlink::load_ncbi_to_hgnc(&path)?;
+
+        assert_eq!(map.len(), 43792);
+        assert_eq!(map.get(&1), Some(&vec!["HGNC:5".to_string()]));
+        assert_eq!(map.get(&2), Some(&vec!["HGNC:7".to_string()]));
+
+        Ok(())
+    }
+}