gncttr/gncttr.rs gelöscht
This commit is contained in:
parent
160ee53433
commit
097f5c1a5b
1 changed files with 0 additions and 241 deletions
241
gncttr/gncttr.rs
241
gncttr/gncttr.rs
|
|
@ -1,241 +0,0 @@
|
|||
#![allow(unstable)] // allow unstable libraries
|
||||
#![feature(rustc_private)]
|
||||
|
||||
#[macro_use] extern crate lazy_static;
|
||||
|
||||
extern crate regex;
|
||||
|
||||
use std::io;
|
||||
use std::io::prelude::*;
|
||||
//use chomp::primitives::Primitives;
|
||||
use std::collections::HashMap;
|
||||
use regex::Regex;
|
||||
use regex::Error;
|
||||
|
||||
|
||||
/// 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>
|
||||
let starts : [String; 3] = [format!("ATG"), format!("TTG"), format!("CTG")]; // array -> fixed size!
|
||||
let limit = 100000; // length limitation for analysed sequence window
|
||||
|
||||
// regex for identication of nucleodide
|
||||
// let nc_pattern = r"[ATCGN]";
|
||||
// let res = Regex::new(nc_pattern);
|
||||
|
||||
// translate codon into AS
|
||||
/* let t = "TTT".to_string();
|
||||
let AS = code.get(&t);
|
||||
println!("AS for {} is {}", t, AS.unwrap());
|
||||
if let Ok(regex) = res {
|
||||
println!("regex ok, trying to match..");
|
||||
let matches = regex.is_match(&t);
|
||||
if matches {
|
||||
println!("{} is nucleotid {}", t, nc_pattern);
|
||||
} else {
|
||||
println!("{} NOT a nucleotid sequence {}", t, nc_pattern);
|
||||
}
|
||||
} else {
|
||||
println!("{:?}", res);
|
||||
}
|
||||
*/
|
||||
|
||||
// playing with regex
|
||||
let nc_pattern = Regex::new(r"[ATCGN]").unwrap(); // assign regex
|
||||
let head = Regex::new(r"^>(.*)").unwrap(); // regex for capturing header
|
||||
let test = ">wppwpweATTCGTGC8023582305";
|
||||
// let after = re.replace_all(test, "--");
|
||||
// println!("{}", after);
|
||||
/* for cap in re.captures_iter(test) {
|
||||
println!("{} -> {} -> {}", &cap[0], &cap[1], &cap[2]); // &cap[0] -> all captured by regex, &cap[1] -> 1st captured group, &cap[2] -> 2nd captured group, ...
|
||||
}
|
||||
*/
|
||||
/* for cap in head.captures_iter(test) {
|
||||
println!("Header: {}", &cap[1]);
|
||||
}
|
||||
*/
|
||||
|
||||
//let matches = re.is_match(&test);
|
||||
//assert!(re.is_match("TCGN"));
|
||||
|
||||
// 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().to_string();
|
||||
let h = head.is_match(&read); // fasta header?
|
||||
let nt = nc_pattern.is_match(&read); // nucleotide sequences?
|
||||
if h {
|
||||
//eprintln!("HEADER found! {}", read);
|
||||
} else if nt {
|
||||
//eprintln!("NUCLEOTIDE sequences {}", read);
|
||||
chomp(&mut read);
|
||||
//println!("{}", read.len()); // 80 nt
|
||||
seq.push_str(&read);
|
||||
if seq.len() > limit {
|
||||
//let codons = triple(&seq);
|
||||
println!("{}", seq.len());
|
||||
seq = seq[81..(seq.len() - 81)].to_string();
|
||||
}
|
||||
|
||||
// search for startcodon in seq
|
||||
|
||||
// search for stopcodon in seq
|
||||
|
||||
// start & stopcodon?? -> get sequence!
|
||||
|
||||
//seq.push_str(&read); // concatenate strings
|
||||
//println!("{}", seq);
|
||||
} else {
|
||||
eprintln!("[ERROR]\tskipping line because of non-nucleotid sequence!");
|
||||
continue;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
// split sequence into codons
|
||||
/* let codons = triple(&seq);
|
||||
for &c in codons.iter() {
|
||||
//println!("{}", c);
|
||||
|
||||
// find startcodon
|
||||
//let ini = starts.iter().position(|r| r == c).unwrap();
|
||||
//println!("{}", ini);
|
||||
|
||||
// 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;
|
||||
}
|
||||
Loading…
Add table
Add a link
Reference in a new issue