gncttr, a nucleotide translation tool for search of coding sequences
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2 changed files with 212 additions and 7 deletions
182
gncttr/gncttr.rs
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182
gncttr/gncttr.rs
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#![allow(unstable)] // allow unstable libraries
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#![feature(rustc_private)]
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#[macro_use]
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extern crate chomp;
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use std::io;
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use std::io::prelude::*;
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//use chomp::primitives::Primitives;
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use std::collections::HashMap;
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/// write: how compiled? how run programm? which parameters for programm call?
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// cat gncttr/*fna | cargo run --
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// programm for extraction of codon sequences from genoms
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fn main () {
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// fill hash with genetic code
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let mut code = HashMap::new();
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code = gencode(); // HashMap<String, String>
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/* // translate codon into AS
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let t = "TTT".to_string();
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let AS = code.get(&t);
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println!("AS for {} is {}", t, AS.unwrap());
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*/
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/* for key in code.keys() {
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println!("{}", key);
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}
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for val in code.values() {
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println!("{}", val);
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}
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for (key, val) in code.iter() {
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println!("{} {}", key, val);
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}
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*/
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// read sequence from stdin
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let stdin = io::stdin();
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let mut seq = String::new();
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for mut line in stdin.lock().lines() {
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let mut read = line.unwrap();
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chomp(&mut read);
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seq.push_str(&read); // concatenate strings
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//println!("{}", seq);
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}
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// split sequence into codons
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let codons = triple(&seq);
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for &c in codons.iter() {
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//println!("{}", c);
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// translate codons
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let AS = code.get(c);
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match AS {
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Some(AS) => println!("{}", AS),
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None => println!("Something went wrong!!\n{} is no codon!", c), //println!("AS for codon {} is {}!", c, AS);
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}
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}
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// clean sequence -> remove header (![ATCGNU])
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/* // remove newline
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let mut test = format!("test\n");
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let dummy = format!("dummy1");
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//println!("{}", test);
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//rm_newline(&test);
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//test.pop();
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chomp(&mut test);
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//println!("{}", test);
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test.push_str(&dummy);
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println!("{}", test);
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*/
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// split sequence into triplet
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// compare & translate triplet into AS
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// CDS??
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// print out CDS
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}
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// remove newline character from string
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fn triple (string: &str) -> Vec<&str> {
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// split into triplets
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let mut triplet = String::new();
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let mut codon: Vec<&str> = Vec::new();;
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for (i, s) in string.chars().enumerate() {
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if i%3 == 0 {
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codon.push(&string[(i)..(i+3)]);
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triplet = format!(""); // empty string
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}
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triplet.push(s);
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}
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codon
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}
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// remove newline character at end of string // rebuild of trim_right_matches("\n")
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fn chomp(raw: &mut String) {
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let last = raw.chars().last().unwrap();
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//println!("last character of string is: {}", last);
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if last == '\n' {
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eprintln!("[INFO]\tNewline removed!");
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raw.pop();
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};
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}
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// create hash containing genetic code
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fn gencode() -> (HashMap<String, String>) {
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let mut code = HashMap::new();
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code.insert("TTT".to_string(), "F".to_string());
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code.insert("TTC".to_string(), "F".to_string());
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code.insert("TTA".to_string(), "L".to_string());
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code.insert("TTG".to_string(), "L".to_string());
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code.insert("TCT".to_string(), "S".to_string());
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code.insert("TCC".to_string(), "S".to_string());
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code.insert("TCA".to_string(), "S".to_string());
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code.insert("TCG".to_string(), "S".to_string());
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code.insert("TAT".to_string(), "Y".to_string());
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code.insert("TAC".to_string(), "Y".to_string());
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code.insert("TAA".to_string(), "*".to_string());
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code.insert("TAG".to_string(), "*".to_string());
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code.insert("TGT".to_string(), "C".to_string());
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code.insert("TGC".to_string(), "C".to_string());
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code.insert("TGA".to_string(), "*".to_string());
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code.insert("TGG".to_string(), "W".to_string());
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code.insert("CTT".to_string(), "L".to_string());
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code.insert("CTC".to_string(), "L".to_string());
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code.insert("CTA".to_string(), "L".to_string());
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code.insert("CTG".to_string(), "L".to_string());
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code.insert("CCT".to_string(), "P".to_string());
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code.insert("CCC".to_string(), "P".to_string());
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code.insert("CCA".to_string(), "P".to_string());
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code.insert("CCG".to_string(), "P".to_string());
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code.insert("CAT".to_string(), "H".to_string());
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code.insert("CAC".to_string(), "H".to_string());
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code.insert("CAA".to_string(), "Q".to_string());
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code.insert("CAG".to_string(), "Q".to_string());
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code.insert("CGT".to_string(), "R".to_string());
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code.insert("CGC".to_string(), "R".to_string());
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code.insert("CGA".to_string(), "R".to_string());
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code.insert("CGG".to_string(), "R".to_string());
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code.insert("ATT".to_string(), "I".to_string());
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code.insert("ATC".to_string(), "I".to_string());
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code.insert("ATA".to_string(), "I".to_string());
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code.insert("ACT".to_string(), "T".to_string());
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code.insert("ACC".to_string(), "T".to_string());
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code.insert("ACA".to_string(), "T".to_string());
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code.insert("ACG".to_string(), "T".to_string());
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code.insert("AAT".to_string(), "N".to_string());
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code.insert("AAC".to_string(), "N".to_string());
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code.insert("ATG".to_string(), "M".to_string());
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code.insert("AAA".to_string(), "K".to_string());
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code.insert("AAG".to_string(), "K".to_string());
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code.insert("AGT".to_string(), "S".to_string());
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code.insert("AGC".to_string(), "S".to_string());
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code.insert("AGA".to_string(), "R".to_string());
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code.insert("AGG".to_string(), "R".to_string());
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code.insert("GTT".to_string(), "V".to_string());
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code.insert("GTC".to_string(), "V".to_string());
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code.insert("GTA".to_string(), "V".to_string());
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code.insert("GTG".to_string(), "V".to_string());
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code.insert("GCT".to_string(), "A".to_string());
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code.insert("GCC".to_string(), "A".to_string());
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code.insert("GCA".to_string(), "A".to_string());
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code.insert("GCG".to_string(), "A".to_string());
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code.insert("GAT".to_string(), "D".to_string());
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code.insert("GAC".to_string(), "D".to_string());
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code.insert("GAA".to_string(), "E".to_string());
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code.insert("GAG".to_string(), "E".to_string());
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code.insert("GGT".to_string(), "G".to_string());
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code.insert("GGC".to_string(), "G".to_string());
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code.insert("GGA".to_string(), "G".to_string());
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code.insert("GGG".to_string(), "G".to_string());
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return code;
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}
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// functions
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// print help menu
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fn print_usage(program: &str, opts: Options) {
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let brief = format!("Usage: {} FILE [options]", program);
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@ -59,6 +57,25 @@ fn filler () -> Vec<char> {
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return signs
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}
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// fill vector with special character only
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fn spcl () -> Vec<char> {
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let mut special: Vec<char> = vec![];
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// fill vector with special character
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for i in 33u8..47u8 {
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special.push(i as char)
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}
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for i in 58u8..64u8 {
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special.push(i as char)
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}
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for i in 91u8..96u8 {
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special.push(i as char)
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}
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for i in 123u8..126u8 {
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special.push(i as char)
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}
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return special
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}
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// creation of passward with certain length
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fn pw (pass_length: &usize, signs: &Vec<char>) -> String {
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let mut password = String::new(); // assign password as empty string
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//let test: char = '5';
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//println!("first {}", control);
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let mut special: Vec<char> = spcl(); // fill vector with special character
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let mut lowcase = 0; // counter for lowercase
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let mut upcase = 0; // counter for upptercase
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let uprex = Regex::new(r"[A-Z]").unwrap(); // regex uppercase
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let lowex = Regex::new(r"[a-z]").unwrap();// regex lowercase
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assert!(uprex.is_match("A")); // testing regex
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assert!(lowex.is_match("b"));
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//assert!(uprex.is_match("A")); // testing regex
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//assert!(lowex.is_match("b"));
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/*for i in &special {
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println!("{}", i);
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}*/
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let mut dup: f64 = 0.0; // number of same character in row
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// verification of password
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@ -156,13 +177,15 @@ fn main() {
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// different cases
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let cstr = c.to_string(); // convert <char> into <String>
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if uprex.is_match(&cstr) {
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println!("uppercase letter {}", c);
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//println!("uppercase letter {}", c);
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upcase = 1;
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} else if lowex.is_match(&cstr) {
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println!("lowercase letter {}", c);
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//println!("lowercase letter {}", c);
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lowcase = 1;
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}
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// special character??
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//println!("{} vs {}", control, c);
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control = c.clone();
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}
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