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#![recursion_limit = "1024"]
#[macro_use]
extern crate error_chain;
extern crate indextree;
mod errors {
error_chain! {
foreign_links {
Io(::std::io::Error) #[doc = "Io"];
ParseIntError(::std::num::ParseIntError);
}
errors {
NodeFileFormatError(l: String) {
description("format error in nodes.dmp file")
display("format error in nodes.dmp in line {}", l)
}
}
}
}
use self::errors::*;
use std::collections::HashMap;
use std::fs::File;
use std::io::{BufReader,BufRead};
use indextree::{Arena, NodeId, Traverse};
pub use indextree::NodeEdge;
#[derive(Debug)]
pub struct NcbiTaxonomy {
arena: Arena<u32>,
name_to_node: HashMap<String, NodeId>,
id_to_node: HashMap<u32, NodeId>,
id_to_name: HashMap<u32, String>,
}
impl NcbiTaxonomy {
pub fn from_ncbi_files(nodes_filename: &str, names_filename: &str) -> Result<NcbiTaxonomy> {
let mut child_ids_by_parent_id: HashMap<u32, Vec<u32>> = HashMap::new();
let nodes_file = File::open(nodes_filename)?;
for line_maybe in BufReader::new(nodes_file).lines() {
match line_maybe {
Ok(line) => {
let mut fields = line.split("\t|\t");
let id_str = fields.next().chain_err(|| ErrorKind::NodeFileFormatError(line.clone()))?;
let parent_id_str = fields.next().chain_err(|| ErrorKind::NodeFileFormatError(line.clone()))?;
let id = id_str.parse::<u32>().chain_err(|| format!("failed to parse id_str as u32: {}", id_str))?;
let parent_id = parent_id_str.parse::<u32>().chain_err(|| format!("failed to parse parent_id_str as u32: {}", parent_id_str))?;
if parent_id != id { child_ids_by_parent_id.entry(parent_id).or_insert_with(Vec::new).push(id);
}
},
Err(e) => return Err(ErrorKind::Io(e).into())
}
}
let mut keys = child_ids_by_parent_id.keys().collect::<Vec<&u32>>();
keys.sort_unstable_by(|a, b| a.cmp(b));
let mut arena: Arena<u32> = Arena::new();
let mut id_to_node: HashMap<u32, NodeId> = HashMap::new();
for id in keys {
let node_id = match id_to_node.get(id) {
Some(node_id) => *node_id,
None => arena.new_node(*id),
};
id_to_node.insert(*id, node_id);
for child in child_ids_by_parent_id.get(&id).expect("ID not found in child_ids_by_parent_id") {
let child_node_id = match id_to_node.get(child) {
Some(child_node_id) => *child_node_id,
None => arena.new_node(*child),
};
id_to_node.insert(*child, child_node_id);
assert_ne!(node_id, child_node_id, "child node id same as node: {} (for {} {})", node_id, *id, *child);
node_id.append(child_node_id, &mut arena).unwrap(); }
}
let mut name_to_node = HashMap::new();
let mut id_to_name = HashMap::new();
let name_file = File::open(names_filename)?;
for line_maybe in BufReader::new(name_file).lines() {
let line = match line_maybe {
Ok(line) => line,
Err(e) => return Err(ErrorKind::Io(e).into())
};
let mut fields = line.split("\t|\t").collect::<Vec<&str>>();
if fields[3].starts_with("scientific name") {
let id_str = fields[0];
let id = id_str.parse::<u32>().chain_err(|| format!("failed to parse id_str as u32: {}", id_str))?;
let name = fields[1].to_string();
let node_id = id_to_node.get(&id).expect("ID not found in id_to_node");
id_to_name.insert(id, name.clone());
name_to_node.insert(name, *node_id);
}
}
let tree = NcbiTaxonomy { arena, name_to_node, id_to_node, id_to_name };
Ok(tree)
}
pub fn contains_id(&self, id: u32) -> bool {
self.id_to_node.contains_key(&id)
}
pub fn contains_name(&self, name: &str) -> bool {
self.name_to_node.contains_key(name)
}
pub fn is_descendant(&self, name: &str, ancestor_name: &str) -> bool {
let id = match self.name_to_node.get(name) {
Some(id) => id,
None => return false
};
let ancestor_id = match self.name_to_node.get(ancestor_name) {
Some(id) => id,
None => return false
};
for node in id.ancestors(&self.arena) {
if node == *ancestor_id {
return true
}
}
false
}
pub fn get_node_by_id(&self, id: u32) -> Option<&NodeId> {
self.id_to_node.get(&id)
}
pub fn traversal(&self, from: u32) -> Option<Traverse<u32>> {
match self.get_node_by_id(from) {
Some(node_id) => Some(node_id.traverse(&self.arena)),
None => None
}
}
pub fn get_id_by_node(&self, node_id: NodeId) -> Option<u32> {
match self.arena.get(node_id) {
Some(node) => Some(node.data),
None => None
}
}
pub fn get_name_by_id(&self, id: u32) -> Option<&String> {
self.id_to_name.get(&id)
}
}
#[cfg(test)]
mod tests {
use super::{NcbiTaxonomy, NodeEdge};
pub struct NcbiTaxonomyFixture {
pub taxonomy: NcbiTaxonomy,
}
impl Default for NcbiTaxonomyFixture {
fn default() -> Self {
let tree = NcbiTaxonomy::from_ncbi_files("data/sample_tree_nodes.dmp", "data/sample_tree_names.dmp").unwrap();
Self { taxonomy: tree }
}
}
#[test]
fn contains_id() {
let fixture = NcbiTaxonomyFixture::default();
assert!(fixture.taxonomy.contains_id(504556));
}
#[test]
fn contains_name() {
let fixture = NcbiTaxonomyFixture::default();
assert!(fixture.taxonomy.contains_name("Propionibacterium phage PAS7"));
assert!(fixture.taxonomy.contains_name("Viruses"));
assert!(fixture.taxonomy.contains_name("environmental samples"));
}
#[test]
fn get_node_by_id() {
let fixture = NcbiTaxonomyFixture::default();
assert_eq!(fixture.taxonomy.get_node_by_id(999999999), None);
assert!(match fixture.taxonomy.get_node_by_id(504556) { Some(_) => true, None => false })
}
#[test]
fn get_id_by_node() {
let fixture = NcbiTaxonomyFixture::default();
let node_id = fixture.taxonomy.get_node_by_id(504556).unwrap();
assert_eq!(fixture.taxonomy.get_id_by_node(*node_id).unwrap(), 504556);
}
#[test]
fn get_name_by_id() {
let fixture = NcbiTaxonomyFixture::default();
assert_eq!(fixture.taxonomy.get_name_by_id(370556).unwrap(), "Streptococcus phage 9429.1");
}
#[test]
fn traversal() {
let fixture = NcbiTaxonomyFixture::default();
let traversal = fixture.taxonomy.traversal(12333);
match traversal {
Some(traversal) => {
let mut counter = 0;
for node_edge in traversal {
match node_edge {
NodeEdge::Start(_) => counter += 1,
_ => ()
}
}
assert_eq!(counter, 500)
}
None => assert_eq!(true, false, "Failed to load traversal from 12333")
}
}
#[test]
fn descendants() {
let fixture = NcbiTaxonomyFixture::default();
assert!(fixture.taxonomy.is_descendant("Propionibacterium phage PAS7", "unclassified bacterial viruses"));
}
}