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https://github.com/pcvolkmer/fastq-tools.git
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Initial commit
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285
src/main.rs
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285
src/main.rs
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@@ -0,0 +1,285 @@
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use std::{fmt::Display, str::FromStr};
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use regex::Regex;
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struct Header {
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instrument_name: String,
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run_id: u32,
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flowcell_id: String,
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flowcell_lane: u32,
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tile_number: u32,
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x: u32,
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y: u32,
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pair_member: Pair,
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filtered: Filtered,
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control_bits: u32,
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index_sequence: String,
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}
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fn scramble_sequence(value: &str, seed: u32) -> String {
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let ahead_1 = Regex::new(r"T([ACG])").unwrap();
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let ahead_2 = Regex::new(r"A([CGT])").unwrap();
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let ahead_3 = Regex::new(r"G([ACT])").unwrap();
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let ahead_4 = Regex::new(r"C([AGT])").unwrap();
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let mut chars = value.chars().collect::<Vec<_>>();
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(1..value.len()).for_each(|idx| {
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if idx % (1 + (seed % 3) as usize) == 0 && chars[idx] > chars[idx - 1] {
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chars.swap(idx, idx - 1);
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}
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});
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let mut result = chars.iter().collect::<String>();
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ahead_1.find_iter(value).for_each(|m| {
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if !m.is_empty() {
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result.replace_range(m.start()..m.end(), "CT")
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}
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});
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ahead_2.find_iter(value).for_each(|m| {
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if !m.is_empty() && seed % 2 != 0 {
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result.replace_range(m.start()..m.end(), "GA")
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}
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});
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ahead_3.find_iter(value).for_each(|m| {
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if !m.is_empty() && seed % 3 != 0 {
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result.replace_range(m.start()..m.end(), "CG")
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}
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});
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ahead_4.find_iter(value).for_each(|m| {
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if !m.is_empty() && seed % 5 != 0 {
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result.replace_range(m.start()..m.end(), "GC")
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}
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});
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result.to_string()
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}
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impl Header {
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fn scramble(self) -> Self {
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fn number(value: u32) -> u32 {
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value % 3 + value % 17 + value % 271 + value % 911
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}
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fn string(value: &str) -> String {
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value
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.chars()
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.map(|c| (((c as u8 % 3 * c as u8 % 17) % 26) + 0x41) as char)
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.collect::<String>()
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}
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fn string_sum(value: &str) -> u8 {
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((value.len() as u8) + value.chars().map(|c| c as u8 & 2).sum::<u8>()) % 97
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}
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Header {
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instrument_name: format!("TEST{:0<2}", (string_sum(&self.instrument_name) * 17) % 97),
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run_id: number(self.run_id),
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flowcell_id: string(&self.flowcell_id),
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flowcell_lane: number(self.flowcell_lane),
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tile_number: number(self.tile_number),
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x: self.x + string_sum(&self.instrument_name) as u32,
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y: self.y + string_sum(&self.instrument_name) as u32,
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pair_member: self.pair_member,
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filtered: self.filtered,
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control_bits: self.control_bits,
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index_sequence: scramble_sequence(&self.index_sequence, 1),
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}
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}
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}
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impl Display for Header {
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fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
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write!(
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f,
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"@{}:{}:{}:{}:{}:{}:{} {}:{}:{}:{}",
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self.instrument_name,
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self.run_id,
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self.flowcell_id,
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self.flowcell_lane,
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self.tile_number,
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self.x,
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self.y,
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match self.pair_member {
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Pair::PairedEnd => "1",
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Pair::MatePair => "2",
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},
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match self.filtered {
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Filtered::Y => "Y",
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Filtered::N => "N",
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},
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self.control_bits,
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self.index_sequence
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)
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}
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}
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impl FromStr for Header {
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type Err = String;
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fn from_str(s: &str) -> Result<Self, Self::Err> {
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if !s.starts_with("@") {
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return Err("Invalid Casava 1.8+ header".to_string());
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}
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let parts = s
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.split(" ")
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.flat_map(|main_part| main_part.split(":").collect::<Vec<_>>())
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.collect::<Vec<_>>();
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if parts.len() != 11 {
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return Err("Invalid Casava 1.8+ header".to_string());
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}
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Ok(Header {
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instrument_name: parts[0][1..].to_string(),
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run_id: parts[1]
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.parse()
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.expect("Valid Casava 1.8+ header: Number value required"),
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flowcell_id: parts[2].into(),
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flowcell_lane: parts[3]
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.parse()
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.expect("Valid Casava 1.8+ header: Number value required"),
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tile_number: parts[4]
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.parse()
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.expect("Valid Casava 1.8+ header: Number value required"),
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x: parts[5]
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.parse()
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.expect("Valid Casava 1.8+ header: Number value required"),
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y: parts[6]
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.parse()
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.expect("Valid Casava 1.8+ header: Number value required"),
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pair_member: match parts[7] {
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"1" => Pair::PairedEnd,
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"2" => Pair::MatePair,
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_ => return Err("Invalid Casava 1.8+ header".to_string()),
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},
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filtered: match parts[8] {
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"Y" => Filtered::Y,
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"N" => Filtered::N,
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_ => return Err("Invalid Casava 1.8+ header".to_string()),
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},
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control_bits: if parts[9]
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.parse::<u32>()
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.expect("Valid Casava 1.8+ header: Even value for control bits required")
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% 2
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== 0
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{
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parts[9].parse().expect("Number")
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} else {
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return Err("Invalid Casava 1.8+ header".to_string());
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},
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index_sequence: parts[10].into(),
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})
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}
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}
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#[derive(Debug, PartialEq)]
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enum Pair {
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PairedEnd = 1,
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MatePair = 2,
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}
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#[derive(Debug, PartialEq)]
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enum Filtered {
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Y,
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N,
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}
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fn main() {
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let stdin = std::io::stdin();
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let mut buf = String::new();
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let mut line = 1;
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while let Ok(n) = stdin.read_line(&mut buf) {
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if n == 0 {
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break;
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}
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if buf.starts_with("@") {
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print!("{}", buf.parse::<Header>().unwrap().scramble())
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} else if buf.starts_with("+") {
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println!("+")
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} else if line % 4 == 0 {
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print!("{buf}")
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} else if line % 4 == 2 {
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print!("{}", scramble_sequence(&buf, line % 97))
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}
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line += 1;
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buf.clear();
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}
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println!()
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}
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#[cfg(test)]
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mod tests {
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use crate::{scramble_sequence, Filtered, Header, Pair};
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#[test]
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fn should_return_parsed_header() {
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let given = "@EAS139:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG";
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let actual = given.parse::<Header>();
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assert!(actual.is_ok());
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let actual = actual.unwrap();
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assert_eq!(actual.instrument_name, "EAS139");
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assert_eq!(actual.run_id, 136);
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assert_eq!(actual.flowcell_id, "FC706VJ");
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assert_eq!(actual.flowcell_lane, 2);
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assert_eq!(actual.tile_number, 2104);
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assert_eq!(actual.x, 15343);
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assert_eq!(actual.y, 197393);
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assert_eq!(actual.pair_member, Pair::PairedEnd);
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assert_eq!(actual.filtered, Filtered::Y);
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assert_eq!(actual.control_bits, 18);
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assert_eq!(actual.index_sequence, "ATCACG");
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}
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#[test]
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fn should_return_header_string() {
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let given = "@EAS139:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG";
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let actual = given.parse::<Header>();
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assert!(actual.is_ok());
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let actual = actual.unwrap();
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assert_eq!(given, actual.to_string());
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}
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#[test]
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fn should_return_scrambled_header_string() {
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let given = "@EAS139:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG";
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let actual = given.parse::<Header>();
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let expected = "@TEST73:273:CQEAACM:8:503:15353:197403 1:Y:18:GAGCGC";
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assert!(actual.is_ok());
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let actual = actual.unwrap().scramble();
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assert_eq!(expected, actual.to_string().as_str());
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}
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#[test]
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fn should_return_scrambled_sequence_string_seed1() {
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let given = "GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT";
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let actual = scramble_sequence(given, 1);
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let expected = "CGATCTGGCGCGCAGCGCCGGAGCGAGCAGAGCGTAGATGCATCCGCGCGGCGCGCCGTT";
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assert_eq!(expected, actual);
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}
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#[test]
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fn should_return_scrambled_sequence_string_seed42() {
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let given = "GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT";
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let actual = scramble_sequence(given, 42);
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let expected = "GTTTCTGGTTCGCAGCGCTCTCGCTCGCATCTTCTATCTGCTTCTTCGCCGCGCGCTTTA";
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assert_eq!(expected, actual);
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}
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}
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