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use debruijn::dna_string::DnaString;
use flate2::read::MultiGzDecoder;
use io_utils::open_for_read;
use std::process::Command;
use std::{io::prelude::*, path::Path};
use string_utils::TextUtils;
pub fn read_fasta_to_vec_vec_u8(f: impl AsRef<Path>) -> Vec<Vec<u8>> {
let mut x = Vec::<Vec<u8>>::new();
let f = f.as_ref();
match f.extension() {
Some(ex) if ex != "gz" => {
let fin = open_for_read![f];
let mut last: String = String::new();
let mut first = true;
for line in fin.lines() {
let s = line.unwrap();
if first {
if !s.starts_with('>') {
panic!("fasta format failure reading {}", f.to_string_lossy());
}
first = false;
x.push(s.get(1..).unwrap().as_bytes().to_vec());
} else if s.starts_with('>') {
x.push(last.as_bytes().to_vec());
last.clear();
x.push(s.get(1..).unwrap().as_bytes().to_vec());
} else {
last += &s;
}
}
x.push(last.as_bytes().to_vec());
}
_ => {
let gz = MultiGzDecoder::new(std::fs::File::open(&f).unwrap());
let fin = std::io::BufReader::new(gz);
let mut last: String = String::new();
let mut first = true;
for line in fin.lines() {
let s = line.unwrap();
if first {
if !s.starts_with('>') {
panic!("fasta format failure");
}
first = false;
x.push(s.get(1..).unwrap().as_bytes().to_vec());
} else if s.starts_with('>') {
x.push(last.as_bytes().to_vec());
last.clear();
x.push(s.get(1..).unwrap().as_bytes().to_vec());
} else {
last += &s;
}
}
x.push(last.as_bytes().to_vec());
}
};
x
}
pub fn read_fasta_into_vec_dna_string_plus_headers(
f: impl AsRef<Path>,
dv: &mut Vec<DnaString>,
headers: &mut Vec<String>,
) {
let f = f.as_ref();
match f.extension() {
Some(ex) if ex == "gz" => {
let fin = open_for_read![f];
let mut last: String = String::new();
let mut first = true;
for line in fin.lines() {
let s = line.unwrap();
if first {
if !s.starts_with('>') {
panic!("fasta format failure reading {}", f.to_string_lossy());
}
first = false;
headers.push(s.get(1..).unwrap().to_string());
} else if s.starts_with('>') {
dv.push(DnaString::from_dna_string(&last));
last.clear();
headers.push(s.get(1..).unwrap().to_string());
} else {
last += &s;
}
}
dv.push(DnaString::from_dna_string(&last));
}
_ => {
let gz = MultiGzDecoder::new(std::fs::File::open(&f).unwrap());
let fin = std::io::BufReader::new(gz);
let mut last: String = String::new();
let mut first = true;
for line in fin.lines() {
let s = line.unwrap();
if first {
if !s.starts_with('>') {
panic!("fasta format failure");
}
first = false;
headers.push(s.get(1..).unwrap().to_string());
} else if s.starts_with('>') {
dv.push(DnaString::from_dna_string(&last));
last.clear();
headers.push(s.get(1..).unwrap().to_string());
} else {
last += &s;
}
}
dv.push(DnaString::from_dna_string(&last));
}
};
}
pub fn read_fasta_contents_into_vec_dna_string_plus_headers(
f: &str,
dv: &mut Vec<DnaString>,
headers: &mut Vec<String>,
) {
let mut last: String = String::new();
let mut first = true;
let lines = f.split('\n').collect::<Vec<&str>>();
for i in 0..lines.len() {
let s = &lines[i];
if first {
if !s.starts_with('>') {
panic!("fasta format failure reading {}", f);
}
first = false;
headers.push(s.get(1..).unwrap().to_string());
} else if s.starts_with('>') {
dv.push(DnaString::from_dna_string(&last));
last.clear();
headers.push(s.get(1..).unwrap().to_string());
} else {
last += s;
}
}
dv.push(DnaString::from_dna_string(&last));
}
pub fn read_fasta_headers(f: impl AsRef<Path>, headers: &mut Vec<String>) {
let f = f.as_ref();
let fin = open_for_read![f];
let mut last: String = String::new();
let mut first = true;
for line in fin.lines() {
let s = line.unwrap();
if first {
if !s.starts_with('>') {
panic!("fasta format failure reading {}", f.to_string_lossy());
}
first = false;
headers.push(s.get(1..).unwrap().to_string());
} else if s.starts_with('>') {
last.clear();
headers.push(s.get(1..).unwrap().to_string());
} else {
last += &s;
}
}
}
pub fn load_genbank_accession(accession: &str, bases: &mut DnaString) {
let link = format!(
"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/\
efetch.fcgi?db=nucleotide&id={}&rettype=fasta",
accession
);
let o = Command::new("csh")
.arg("-c")
.arg(format!("curl \"{}\"", link))
.output()
.expect("failed to execute curl command");
let fasta = String::from_utf8(o.stdout).expect("Response was not valid utf-8.");
let mut fasta = fasta.after("\n").to_string();
assert!(!fasta.contains("moved"));
fasta = fasta.replace("\n", "");
*bases = DnaString::from_dna_string(&fasta);
}
