gncttr, a nucleotide translation tool for search of coding sequences

gncttr/gncttr.rs

@@ -0,0 +1,182 @@
+#![allow(unstable)] // allow unstable libraries
+#![feature(rustc_private)] 
+
+#[macro_use]
+extern crate chomp;
+
+use std::io;
+use std::io::prelude::*;
+//use chomp::primitives::Primitives;
+use std::collections::HashMap;
+
+
+/// write: how compiled? how run programm? which parameters for programm call?
+// cat gncttr/*fna | cargo run --
+
+// programm for extraction of codon sequences from genoms
+fn main () {
+	// fill hash with genetic code
+	let mut code = HashMap::new();
+	code = gencode(); // HashMap<String, String>
+	
+/*	// translate codon into AS
+	let t = "TTT".to_string();
+	let AS = code.get(&t);
+	println!("AS for {} is {}", t, AS.unwrap());
+*/
+	
+/*	for key in code.keys() {
+		println!("{}", key);
+	}
+	for val in code.values() {
+		println!("{}", val);
+	}
+	for (key, val) in code.iter() {
+		println!("{} {}", key, val);
+	}
+*/
+	
+	// read sequence from stdin
+	let stdin = io::stdin();
+	let mut seq = String::new();
+	for mut line in stdin.lock().lines() {
+		let mut read = line.unwrap();
+		chomp(&mut read);
+		seq.push_str(&read); // concatenate strings
+		//println!("{}", seq);
+	}
+	
+	// split sequence into codons
+	let codons = triple(&seq);
+	for &c in codons.iter() {
+		//println!("{}", c);
+		// translate codons
+		let AS = code.get(c);
+		match AS {
+			Some(AS) => println!("{}", AS),
+			None 	=> println!("Something went wrong!!\n{} is no codon!", c),		  //println!("AS for codon {} is {}!", c, AS);
+		}
+	}
+	
+	// clean sequence -> remove header (![ATCGNU])
+
+/*	// remove newline
+	let mut test = format!("test\n");
+	let dummy = format!("dummy1");
+	//println!("{}", test);
+	//rm_newline(&test);
+	//test.pop();
+	chomp(&mut test);
+	//println!("{}", test);
+	test.push_str(&dummy);
+	println!("{}", test);
+*/
+	// split sequence into triplet
+	
+	// compare & translate triplet into AS
+	
+	// CDS??
+	
+	
+	// print out CDS
+
+
+}
+
+
+// remove newline character from string
+fn triple (string: &str) -> Vec<&str> {
+	// split into triplets
+	let mut triplet = String::new();
+	let mut codon: Vec<&str> = Vec::new();;
+	for (i, s) in string.chars().enumerate() {
+		if i%3 == 0 {
+			codon.push(&string[(i)..(i+3)]);
+			triplet = format!(""); // empty string
+		}
+		triplet.push(s);
+	}
+	codon
+}
+
+
+// remove newline character at end of string // rebuild of trim_right_matches("\n")
+fn chomp(raw: &mut String) {
+	let last = raw.chars().last().unwrap();
+	//println!("last character of string is: {}", last);
+	if last == '\n' {
+		eprintln!("[INFO]\tNewline removed!");
+		raw.pop();
+	};
+}
+
+
+// create hash containing genetic code
+fn gencode() -> (HashMap<String, String>) {
+	let mut code = HashMap::new();
+	code.insert("TTT".to_string(), "F".to_string());
+	code.insert("TTC".to_string(), "F".to_string());
+	code.insert("TTA".to_string(), "L".to_string()); 
+	code.insert("TTG".to_string(), "L".to_string()); 
+	code.insert("TCT".to_string(), "S".to_string());
+	code.insert("TCC".to_string(), "S".to_string());
+	code.insert("TCA".to_string(), "S".to_string());
+	code.insert("TCG".to_string(), "S".to_string());
+	code.insert("TAT".to_string(), "Y".to_string());
+	code.insert("TAC".to_string(), "Y".to_string());
+	code.insert("TAA".to_string(), "*".to_string());
+	code.insert("TAG".to_string(), "*".to_string());
+	code.insert("TGT".to_string(), "C".to_string());
+	code.insert("TGC".to_string(), "C".to_string());
+	code.insert("TGA".to_string(), "*".to_string());
+	code.insert("TGG".to_string(), "W".to_string());
+	code.insert("CTT".to_string(), "L".to_string());
+	code.insert("CTC".to_string(), "L".to_string());
+	code.insert("CTA".to_string(), "L".to_string());
+	code.insert("CTG".to_string(), "L".to_string());
+	code.insert("CCT".to_string(), "P".to_string());
+	code.insert("CCC".to_string(), "P".to_string());
+	code.insert("CCA".to_string(), "P".to_string());
+	code.insert("CCG".to_string(), "P".to_string());
+	code.insert("CAT".to_string(), "H".to_string());
+	code.insert("CAC".to_string(), "H".to_string());
+	code.insert("CAA".to_string(), "Q".to_string());
+	code.insert("CAG".to_string(), "Q".to_string());
+	code.insert("CGT".to_string(), "R".to_string());
+	code.insert("CGC".to_string(), "R".to_string());
+	code.insert("CGA".to_string(), "R".to_string());
+	code.insert("CGG".to_string(), "R".to_string());
+	code.insert("ATT".to_string(), "I".to_string());
+	code.insert("ATC".to_string(), "I".to_string());
+	code.insert("ATA".to_string(), "I".to_string());
+	code.insert("ACT".to_string(), "T".to_string());
+	code.insert("ACC".to_string(), "T".to_string());
+	code.insert("ACA".to_string(), "T".to_string());
+	code.insert("ACG".to_string(), "T".to_string());
+	code.insert("AAT".to_string(), "N".to_string());
+	code.insert("AAC".to_string(), "N".to_string());
+	code.insert("ATG".to_string(), "M".to_string());
+	code.insert("AAA".to_string(), "K".to_string());
+	code.insert("AAG".to_string(), "K".to_string());
+	code.insert("AGT".to_string(), "S".to_string());
+	code.insert("AGC".to_string(), "S".to_string());
+	code.insert("AGA".to_string(), "R".to_string());
+	code.insert("AGG".to_string(), "R".to_string());
+	code.insert("GTT".to_string(), "V".to_string());
+	code.insert("GTC".to_string(), "V".to_string());
+	code.insert("GTA".to_string(), "V".to_string());
+	code.insert("GTG".to_string(), "V".to_string());
+	code.insert("GCT".to_string(), "A".to_string());
+	code.insert("GCC".to_string(), "A".to_string());
+	code.insert("GCA".to_string(), "A".to_string());
+	code.insert("GCG".to_string(), "A".to_string());
+	code.insert("GAT".to_string(), "D".to_string());
+	code.insert("GAC".to_string(), "D".to_string());
+	code.insert("GAA".to_string(), "E".to_string());
+	code.insert("GAG".to_string(), "E".to_string());
+	code.insert("GGT".to_string(), "G".to_string());
+	code.insert("GGC".to_string(), "G".to_string());
+	code.insert("GGA".to_string(), "G".to_string());
+	code.insert("GGG".to_string(), "G".to_string());
+	return code;
+}

passwordgenerator.rs

@@ -32,8 +32,6 @@ use regex::Regex;
 
 // functions
 
-
-
 // print help menu
 fn print_usage(program: &str, opts: Options) {
     let brief = format!("Usage: {} FILE [options]", program);
@@ -59,6 +57,25 @@ fn filler () -> Vec<char> {
 	return signs
 }
 
+// fill vector with special character only
+fn spcl () -> Vec<char> {
+	let mut special: Vec<char> = vec![];
+	// fill vector with special character
+	for i in 33u8..47u8 {
+		special.push(i as char)
+	}
+	for i in 58u8..64u8 {
+		special.push(i as char)		
+	}
+	for i in 91u8..96u8 {
+		special.push(i as char)		
+	}
+	for i in 123u8..126u8 {
+		special.push(i as char)
+	}
+	return special
+}
+
 // creation of passward with certain length
 fn pw (pass_length: &usize, signs: &Vec<char>) -> String {
 	let mut password = String::new(); // assign password as empty string
@@ -130,12 +147,16 @@ fn main() {
 		//let test: char = '5';
 		//println!("first {}", control);
 
+		let mut special: Vec<char> = spcl(); // fill vector with special character
 		let mut lowcase = 0; // counter for lowercase
 		let mut upcase = 0; // counter for upptercase
 		let uprex = Regex::new(r"[A-Z]").unwrap(); // regex uppercase
 		let lowex = Regex::new(r"[a-z]").unwrap();// regex lowercase
-		assert!(uprex.is_match("A")); // testing regex
+		//assert!(uprex.is_match("A")); // testing regex
-		assert!(lowex.is_match("b")); 
+		//assert!(lowex.is_match("b")); 
+		/*for i in &special {
+			println!("{}", i);
+		}*/
 		
 		let mut dup: f64 = 0.0; // number of same character in row
 		// verification of password
@@ -156,13 +177,15 @@ fn main() {
 			// different cases
 			let cstr = c.to_string(); // convert <char> into <String>
 			if uprex.is_match(&cstr) {
-				println!("uppercase letter {}", c);
+				//println!("uppercase letter {}", c);
 				upcase = 1;
 			} else if lowex.is_match(&cstr) {
-				println!("lowercase letter {}", c);
+				//println!("lowercase letter {}", c);
 				lowcase = 1;				
 			}
-				
+			
+			// special character??
+			
 			//println!("{} vs {}", control, c);
 			control = c.clone();
 		}