From cae47877f64e80b719de69d9d38182020bb367ed Mon Sep 17 00:00:00 2001
From: rav4s <ravidhruvishshah@gmail.com>
Date: Sat, 20 Feb 2021 17:39:03 -0600
Subject: [PATCH] Added code to break strand into codons and truncate at stop
 codon

---
 src/main.rs | 72 ++++++++++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 69 insertions(+), 3 deletions(-)

diff --git a/src/main.rs b/src/main.rs
index 2a006f3..59973f3 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -1,6 +1,8 @@
 use std::io;
+use std::str;
+use std::process;
 
-fn transcription(dna: String) -> Vec<char> {
+fn transcription(dna: String) -> String {
     let char_vec: Vec<char> = dna.chars().collect();
     let mut transcribed_vec: Vec<char> = Vec::new();
     for i in char_vec {
@@ -10,11 +12,66 @@ fn transcription(dna: String) -> Vec<char> {
             'T' => transcribed_vec.push('A'),
             'C' => transcribed_vec.push('G'),
             'G' => transcribed_vec.push('C'),
-            _ => println!("{}", i) //just print wrong for now
+            _ => {
+                // println!("Incorrect char");
+                break;
+             }
         }
     }
 
-    return transcribed_vec;
+    let transcribed_string: String = transcribed_vec.into_iter().collect();
+    return transcribed_string;
+}
+
+fn find_start(messenger_rna: String) -> String {
+    let start_codon = "AUG";
+    let start_index = messenger_rna.find(start_codon).unwrap();
+    let inter_rna: String = messenger_rna.chars().skip(start_index).collect();
+    return inter_rna;
+}
+
+fn break_into_codons(inter_rna: String) -> Vec<String> {
+    let sub_len = 3;
+    let subs = inter_rna.as_bytes()
+        .chunks(sub_len)
+        .map(str::from_utf8)
+        .collect::<Result<Vec<&str>, _>>()
+        .unwrap();
+
+    let mut string_vec: Vec<String> = Vec::new();
+    for i in &subs {
+        string_vec.push(i.to_string());
+    }
+
+    return string_vec;
+}
+
+fn find_stop(inter_codons: &[String]) -> usize {
+    if inter_codons.iter().any(|i| i == "UAA") {
+        println!("UAA stop codon found!");
+        let stop_index = inter_codons.iter().position(|r| r == "UAA").unwrap();
+        return stop_index;
+    }
+    else if inter_codons.iter().any(|i| i == "UAG") {
+        println!("UAG stop codon found!");
+        let stop_index = inter_codons.iter().position(|r| r == "UAG").unwrap();
+        return stop_index;
+    }
+    else if inter_codons.iter().any(|i| i == "UGA") {
+        println!("UGA stop codon found!");
+        let stop_index = inter_codons.iter().position(|r| r == "UGA").unwrap();
+        return stop_index;
+    }
+    else {
+        println!("No stop codon found!");
+        process::exit(1);
+    }
+}
+
+fn translation(inter_codons: Vec<String>) {
+    for i in inter_codons {
+        println!("{}", i);
+    }
 }
 
 fn main() {
@@ -29,4 +86,13 @@ fn main() {
     strand = strand.to_uppercase();
 
     let messenger_rna = transcription(strand);
+    println!("The transcribed strand is: {}", messenger_rna);
+    let inter_rna = find_start(messenger_rna);
+    println!("{}", inter_rna);
+    let mut inter_codons = break_into_codons(inter_rna);
+    let mut stop_index = find_stop(&inter_codons);
+    stop_index = stop_index + 1;
+    println!("{}", stop_index);
+    inter_codons.truncate(stop_index);
+    translation(inter_codons);
 }