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@tibvdm
tibvdm committed Apr 8, 2024
1 parent d743c0c commit 4eee7ef
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Showing 4 changed files with 189 additions and 84 deletions.
34 changes: 21 additions & 13 deletions sa-mappings/src/functionality.rs
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
//! This module contains the FunctionAggregator struct that is responsible for aggregating the functional annotations of proteins.
//! This module contains the FunctionAggregator struct that is responsible for aggregating the
//! functional annotations of proteins.
use crate::proteins::Protein;

Expand All @@ -7,12 +8,12 @@ pub struct FunctionAggregator {}

impl FunctionAggregator {
/// Aggregates the functional annotations of proteins
///
///
/// # Arguments
/// * `proteins` - A vector of proteins
///
///
/// # Returns
///
///
/// Returns a string containing the aggregated functional annotations
pub fn aggregate(&self, proteins: Vec<Protein>) -> String {
proteins
Expand All @@ -31,21 +32,28 @@ mod tests {
fn test_aggregate() {
let proteins = vec![
Protein {
uniprot_id: "uniprot1".to_string(),
sequence: (0, 3),
taxon_id: 1,
functional_annotations: vec![0xD1, 0x11, 0xA3, 0x8A, 0xD1, 0x27, 0x47, 0x5E, 0x11, 0x99, 0x27],
uniprot_id: "uniprot1".to_string(),
sequence: (0, 3),
taxon_id: 1,
functional_annotations: vec![
0xD1, 0x11, 0xA3, 0x8A, 0xD1, 0x27, 0x47, 0x5E, 0x11, 0x99, 0x27,
]
},
Protein {
uniprot_id: "uniprot2".to_string(),
sequence: (4, 3),
taxon_id: 2,
functional_annotations: vec![0xD1, 0x11, 0xA3, 0x8A, 0xD1, 0x27, 0x47, 0x5E, 0x11, 0x99, 0x27],
uniprot_id: "uniprot2".to_string(),
sequence: (4, 3),
taxon_id: 2,
functional_annotations: vec![
0xD1, 0x11, 0xA3, 0x8A, 0xD1, 0x27, 0x47, 0x5E, 0x11, 0x99, 0x27,
]
},
];

let function_aggregator = FunctionAggregator {};

assert_eq!(function_aggregator.aggregate(proteins), "GO:0009279;IPR:IPR016364;IPR:IPR008816;GO:0009279;IPR:IPR016364;IPR:IPR008816");
assert_eq!(
function_aggregator.aggregate(proteins),
"GO:0009279;IPR:IPR016364;IPR:IPR008816;GO:0009279;IPR:IPR016364;IPR:IPR008816"
);
}
}
6 changes: 3 additions & 3 deletions sa-mappings/src/lib.rs
View file
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
//! This library provides functionality to map protein sequences to their respective taxonomic identifiers
//! and functional annotations.
//! This library provides functionality to map protein sequences to their respective taxonomic
//! identifiers and functional annotations.
#![warn(missing_docs)]

pub mod functionality;
pub mod proteins;
pub mod taxonomy;
pub mod functionality;
118 changes: 82 additions & 36 deletions sa-mappings/src/proteins.rs
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,13 @@
//! This module contains the `Protein` and `Proteins` structs, which are used to represent proteins and collections of proteins, respectively.
//! This module contains the `Protein` and `Proteins` structs, which are used to represent proteins
//! and collections of proteins, respectively.
use std::{error::Error, fs::File, io::BufReader, ops::Index, str::from_utf8};
use std::{
error::Error,
fs::File,
io::BufReader,
ops::Index,
str::from_utf8
};

use bytelines::ByteLines;
use fa_compression::algorithm1::decode;
Expand Down Expand Up @@ -28,7 +35,7 @@ pub struct Protein {
pub taxon_id: TaxonId,

/// The encoded functional annotations of the protein
pub functional_annotations: Vec<u8>,
pub functional_annotations: Vec<u8>
}

/// A struct that represents a collection of proteins
Expand All @@ -38,7 +45,7 @@ pub struct Proteins {
input_string: Vec<u8>,

/// The proteins in the input string
proteins: Vec<Protein>,
proteins: Vec<Protein>
}

impl Protein {
Expand All @@ -50,19 +57,22 @@ impl Protein {

impl Proteins {
/// Creates a new `Proteins` struct from a database file and a `TaxonAggregator`
///
///
/// # Arguments
/// * `file` - The path to the database file
/// * `taxon_aggregator` - The `TaxonAggregator` to use
///
///
/// # Returns
///
///
/// Returns a `Result` containing the `Proteins` struct
///
///
/// # Errors
///
///
/// Returns a `Box<dyn Error>` if an error occurred while reading the database file
pub fn try_from_database_file(file: &str, taxon_aggregator: &TaxonAggregator) -> Result<Self, Box<dyn Error>> {
pub fn try_from_database_file(
file: &str,
taxon_aggregator: &TaxonAggregator
) -> Result<Self, Box<dyn Error>> {
let mut input_string: String = String::new();
let mut proteins: Vec<Protein> = Vec::new();

Expand All @@ -81,7 +91,7 @@ impl Proteins {
let uniprot_id = from_utf8(fields.next().unwrap())?;
let taxon_id = from_utf8(fields.next().unwrap())?.parse::<TaxonId>()?;
let sequence = from_utf8(fields.next().unwrap())?;
let functional_annotations: Vec<u8> = fields.next().unwrap().iter().copied().collect();
let functional_annotations: Vec<u8> = fields.next().unwrap().to_vec();

if !taxon_aggregator.taxon_exists(taxon_id) {
continue;
Expand All @@ -103,23 +113,26 @@ impl Proteins {
input_string.pop();
input_string.push(TERMINATION_CHARACTER.into());

Ok(Self { input_string: input_string.into_bytes(), proteins })
Ok(Self {
input_string: input_string.into_bytes(),
proteins
})
}

/// Returns the sequence of a protein
///
/// # Arguments
/// * `protein` - The protein to get the sequence from
///
///
/// # Returns
///
///
/// Returns a string slice containing the sequence of the protein
pub fn get_sequence(&self, protein: &Protein) -> &str {
let (start, length) = protein.sequence;
let end = start + length as usize;

// unwrap should never fail since the input string will always be utf8
std::str::from_utf8(&self.input_string[start..end]).unwrap()
std::str::from_utf8(&self.input_string[start .. end]).unwrap()
}
}

Expand All @@ -133,32 +146,41 @@ impl Index<usize> for Proteins {

#[cfg(test)]
mod tests {
use std::fs::File;
use std::io::Write;
use std::path::PathBuf;
use std::{
fs::File,

Check warning on line 150 in sa-mappings/src/proteins.rs

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GitHub Actions / Check + test 

the item `File` is imported redundantly
io::Write,
path::PathBuf
};

use fa_compression::algorithm1::decode;

Check warning on line 155 in sa-mappings/src/proteins.rs

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GitHub Actions / Check + test 

the item `decode` is imported redundantly
use tempdir::TempDir;

use crate::taxonomy::AggregationMethod;

use super::*;
use crate::taxonomy::AggregationMethod;

fn create_database_file(tmp_dir: &TempDir) -> PathBuf {
let database_file = tmp_dir.path().join("database.tsv");
let mut file = File::create(&database_file).unwrap();

file.write("P12345\t1\tMLPGLALLLLAAWTARALEV\t".as_bytes()).unwrap();
file.write_all(&[0xD1, 0x11, 0xA3, 0x8A, 0xD1, 0x27, 0x47, 0x5E, 0x11, 0x99, 0x27]).unwrap();
file.write("P12345\t1\tMLPGLALLLLAAWTARALEV\t".as_bytes())
.unwrap();
file.write_all(&[0xD1, 0x11, 0xA3, 0x8A, 0xD1, 0x27, 0x47, 0x5E, 0x11, 0x99, 0x27])
.unwrap();
file.write("\n".as_bytes()).unwrap();
file.write("P54321\t2\tPTDGNAGLLAEPQIAMFCGRLNMHMNVQNG\t".as_bytes()).unwrap();
file.write_all(&[0xD1, 0x11, 0xA3, 0x8A, 0xD1, 0x27, 0x47, 0x5E, 0x11, 0x99, 0x27]).unwrap();
file.write("P54321\t2\tPTDGNAGLLAEPQIAMFCGRLNMHMNVQNG\t".as_bytes())
.unwrap();
file.write_all(&[0xD1, 0x11, 0xA3, 0x8A, 0xD1, 0x27, 0x47, 0x5E, 0x11, 0x99, 0x27])
.unwrap();
file.write("\n".as_bytes()).unwrap();
file.write("P67890\t6\tKWDSDPSGTKTCIDT\t".as_bytes()).unwrap();
file.write_all(&[0xD1, 0x11, 0xA3, 0x8A, 0xD1, 0x27, 0x47, 0x5E, 0x11, 0x99, 0x27]).unwrap();
file.write("P67890\t6\tKWDSDPSGTKTCIDT\t".as_bytes())
.unwrap();
file.write_all(&[0xD1, 0x11, 0xA3, 0x8A, 0xD1, 0x27, 0x47, 0x5E, 0x11, 0x99, 0x27])
.unwrap();
file.write("\n".as_bytes()).unwrap();
file.write("P13579\t17\tKEGILQYCQEVYPELQITNVVEANQPVTIQNWCKRGRKQCKTHPH\t".as_bytes()).unwrap();
file.write_all(&[0xD1, 0x11, 0xA3, 0x8A, 0xD1, 0x27, 0x47, 0x5E, 0x11, 0x99, 0x27]).unwrap();
file.write("P13579\t17\tKEGILQYCQEVYPELQITNVVEANQPVTIQNWCKRGRKQCKTHPH\t".as_bytes())
.unwrap();
file.write_all(&[0xD1, 0x11, 0xA3, 0x8A, 0xD1, 0x27, 0x47, 0x5E, 0x11, 0x99, 0x27])
.unwrap();
file.write("\n".as_bytes()).unwrap();

database_file
Expand Down Expand Up @@ -194,14 +216,23 @@ mod tests {
let database_file = create_database_file(&tmp_dir);
let taxonomy_file = create_taxonomy_file(&tmp_dir);

let taxon_aggregator = TaxonAggregator::try_from_taxonomy_file(taxonomy_file.to_str().unwrap(), AggregationMethod::Lca).unwrap();
let proteins = Proteins::try_from_database_file(database_file.to_str().unwrap(), &taxon_aggregator).unwrap();
let taxon_aggregator = TaxonAggregator::try_from_taxonomy_file(
taxonomy_file.to_str().unwrap(),
AggregationMethod::Lca
)
.unwrap();
let proteins =
Proteins::try_from_database_file(database_file.to_str().unwrap(), &taxon_aggregator)
.unwrap();

//assert_eq!(proteins.proteins.len(), 4);
assert_eq!(proteins.get_sequence(&proteins[0]), "MLPGLALLLLAAWTARALEV");
assert_eq!(proteins.get_sequence(&proteins[1]), "PTDGNAGLLAEPQIAMFCGRLNMHMNVQNG");
assert_eq!(proteins.get_sequence(&proteins[2]), "KWDSDPSGTKTCIDT");
assert_eq!(proteins.get_sequence(&proteins[3]), "KEGILQYCQEVYPELQITNVVEANQPVTIQNWCKRGRKQCKTHPH");
assert_eq!(
proteins.get_sequence(&proteins[3]),
"KEGILQYCQEVYPELQITNVVEANQPVTIQNWCKRGRKQCKTHPH"
);
}

#[test]
Expand All @@ -212,8 +243,14 @@ mod tests {
let database_file = create_database_file(&tmp_dir);
let taxonomy_file = create_taxonomy_file(&tmp_dir);

let taxon_aggregator = TaxonAggregator::try_from_taxonomy_file(taxonomy_file.to_str().unwrap(), AggregationMethod::Lca).unwrap();
let proteins = Proteins::try_from_database_file(database_file.to_str().unwrap(), &taxon_aggregator).unwrap();
let taxon_aggregator = TaxonAggregator::try_from_taxonomy_file(
taxonomy_file.to_str().unwrap(),
AggregationMethod::Lca
)
.unwrap();
let proteins =
Proteins::try_from_database_file(database_file.to_str().unwrap(), &taxon_aggregator)
.unwrap();

let taxa = vec![1, 2, 6, 17];
for (i, protein) in proteins.proteins.iter().enumerate() {
Expand All @@ -229,11 +266,20 @@ mod tests {
let database_file = create_database_file(&tmp_dir);
let taxonomy_file = create_taxonomy_file(&tmp_dir);

let taxon_aggregator = TaxonAggregator::try_from_taxonomy_file(taxonomy_file.to_str().unwrap(), AggregationMethod::Lca).unwrap();
let proteins = Proteins::try_from_database_file(database_file.to_str().unwrap(), &taxon_aggregator).unwrap();
let taxon_aggregator = TaxonAggregator::try_from_taxonomy_file(
taxonomy_file.to_str().unwrap(),
AggregationMethod::Lca
)
.unwrap();
let proteins =
Proteins::try_from_database_file(database_file.to_str().unwrap(), &taxon_aggregator)
.unwrap();

for protein in proteins.proteins.iter() {
assert_eq!(decode(&protein.functional_annotations), "GO:0009279;IPR:IPR016364;IPR:IPR008816");
assert_eq!(
decode(&protein.functional_annotations),
"GO:0009279;IPR:IPR016364;IPR:IPR008816"
);
}
}
}
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