first commit

Cargo.lock

@@ -0,0 +1,335 @@
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Cargo.toml

@@ -0,0 +1,13 @@
+[package]
+name = "corr"
+version = "0.1.0"
+edition = "2021"
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+
+[dependencies]
+
+ndarray = "0.15.6"
+ndarray-stats = "0.5.1"
+rayon = "1.7.0"
+hashbrown = {version = "0.14.0", features = ["rayon"]}

src/main.rs

@@ -0,0 +1,133 @@
+use std::error::Error;
+use std::fs::File;
+use std::io::{BufReader, BufRead};
+use std::sync::{Arc, Mutex};
+
+use rayon::prelude::*;
+use hashbrown::HashMap;
+
+use ndarray::Array2;
+use ndarray_stats::CorrelationExt;
+use std::io::Write;
+
+fn main() -> Result<(), Box<dyn Error>> {
+    let filename = "/Turbine-pool/LAL-T_ChIP/data/all_sub.tsv";
+    let enhancer_prefix = "EH38E";
+
+    let file = File::open(filename)?;
+    let reader = BufReader::new(file);
+
+    let mut rna_set: HashMap<String, Vec<f32>> = HashMap::default();
+    let mut enhancer_set: HashMap<String, Vec<f32>> = HashMap::default();
+
+    for (index, line) in reader.lines().enumerate() {
+        if index == 0 { continue; }
+
+        if let Ok(line) = line {
+            let mut key = String::default();
+            let mut values: Vec<f32> = Vec::new();
+            for (col, item) in line.split('\t').into_iter().enumerate() {
+                match col {
+                    0 => key = item.to_string(),
+                    5.. => values.push(item.parse()?),
+                    _ => ()
+                }
+            }
+
+            if key.starts_with(enhancer_prefix) {
+                enhancer_set.insert(key, values);
+            } else {
+                rna_set.insert(key, values);
+            }
+
+            // if enhancer_set.len() > 2 {
+            //     break;
+            // }
+        }
+    }
+    println!("{} enhancers", enhancer_set.len());
+    println!("{} rnas", rna_set.len());
+
+    // let best_corr: Arc<Mutex<HashMap<String, (f32, Vec<String>)>>> = Arc::new(Mutex::new(HashMap::new()));
+
+    let enhancers_to_rnas: Arc<Mutex<HashMap<String, HashMap<String, f32>>>> = Arc::new(Mutex::new(HashMap::new()));
+
+    enhancer_set.par_iter().for_each(|(a_k, a_v)| {
+
+        let correlations: Arc<Mutex<HashMap<String, f32>>> = Arc::new(Mutex::new(HashMap::new()));
+        println!("correlation for {}", a_k);
+        
+        rna_set.par_iter().for_each(|(b_k, b_v)| {
+
+            let rand_vec = vec![a_v, b_v];
+            let ncols = rand_vec.first().map_or(0, |row| row.len());
+            let mut nrows = 0;
+            let mut data = Vec::new();
+
+            for i in 0..rand_vec.len() {
+                data.extend_from_slice(&rand_vec[i]);
+                nrows += 1;
+            }
+
+            let a: ndarray::ArrayBase<ndarray::OwnedRepr<_>, ndarray::Dim<[usize; 2]>> = Array2::from_shape_vec((nrows, ncols), data).unwrap();
+
+            let corr = a.pearson_correlation().unwrap();
+            let mut correlations_guard = correlations.lock().unwrap();
+            correlations_guard.insert(b_k.clone(), corr.clone().into_raw_vec().into_iter().reduce(f32::min).unwrap());
+
+        });
+
+        let correlations_guard = correlations.lock().unwrap();
+        
+        let mut enhancers_to_rnas_guard = enhancers_to_rnas.lock().unwrap();
+        enhancers_to_rnas_guard.insert(a_k.to_string(), correlations_guard.clone());
+        
+        // let min_value = correlations_guard.values().min_by(|a, b| a.partial_cmp(b).unwrap());
+        // if let Some(min) = min_value {
+        //     let minimal_keys: Vec<String> = correlations_guard
+        //         .iter()
+        //         .filter(|(_, value)| *value == min)
+        //         .map(|(key, _)| key.to_string())
+        //         .collect();
+
+        //     let mut best_corr_guard = best_corr.lock().unwrap();
+        //     best_corr_guard.insert(a_k.to_string(), (*min, minimal_keys));
+            
+        // }
+    });
+
+    let enhancers_to_rnas_guard = enhancers_to_rnas.lock().unwrap();
+    println!("{:?} enhancers results to write...", enhancers_to_rnas_guard.len());
+
+    let mut rna_keys: Vec<&String> = rna_set.keys().collect();
+    rna_keys.sort();
+
+
+    let mut file = File::create("output.tsv")?;
+
+    // Write the header row
+    write!(file, "ID\t")?; 
+    for rna_key in &rna_keys {
+        write!(file, "{}\t", rna_key)?;
+    }
+    writeln!(file)?; // \n
+
+
+    // Iterate over the enhancers
+    for (enhancer, inner_map) in enhancers_to_rnas_guard.iter() {
+        write!(file, "{}\t", enhancer)?;
+
+        // Iterate over the RNA keys
+        for rna_key in &rna_keys {
+            // Write the value if present, otherwise write an empty cell
+            if let Some(value) = inner_map.get(*rna_key) {
+                write!(file, "{}\t", value)?;
+            } else {
+                write!(file, "\t")?;
+            }
+        }
+        writeln!(file)?;
+    }
+
+    Ok(())
+}