1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253
//! GFF reader and iterators.
mod lines;
mod records;
pub use self::{lines::Lines, records::Records};
use std::io::{self, BufRead};
const LINE_FEED: char = '\n';
const CARRIAGE_RETURN: char = '\r';
/// A GFF reader.
pub struct Reader<R> {
inner: R,
}
impl<R> Reader<R>
where
R: BufRead,
{
/// Creates a GFF reader.
///
/// # Examples
///
/// ```
/// use noodles_gff as gff;
/// let data = b"##gff-version 3\n";
/// let mut reader = gff::Reader::new(&data[..]);
/// ```
pub fn new(inner: R) -> Self {
Self { inner }
}
/// Returns a reference to the underlying reader.
///
/// # Examples
///
/// ```
/// use noodles_gff as gff;
///
/// let data = b"##gff-version 3\n";
/// let reader = gff::Reader::new(&data[..]);
///
/// let _ = reader.get_ref();
/// ```
pub fn get_ref(&self) -> &R {
&self.inner
}
/// Unwraps and returns the underlying reader.
///
/// # Examples
///
/// ```
/// # use std::io;
/// use noodles_gff as gff;
///
/// let data = b"##gff-version 3
/// #format: gff3
/// ";
/// let mut reader = gff::Reader::new(&data[..]);
/// reader.read_line(&mut String::new())?;
///
/// assert_eq!(reader.into_inner(), b"#format: gff3\n");
/// # Ok::<_, io::Error>(())
/// ```
pub fn into_inner(self) -> R {
self.inner
}
/// Reads a raw GFF line.
///
/// This reads from the underlying stream until a newline is reached and appends it to the
/// given buffer, sans the final newline character. The buffer can subsequently be parsed as a
/// [`crate::Line`].
///
/// It is more ergonomic to read records using an iterator (see [`Self::lines`]), but using
/// this method allows control of the line buffer and whether the raw line should be parsed.
///
/// If successful, the number of bytes read is returned. If the number of bytes read is 0, the
/// stream reached EOF.
///
/// # Examples
///
/// ```
/// # use std::io;
/// use noodles_gff as gff;
///
/// let data = b"##gff-version 3
/// sq0\tNOODLES\tgene\t8\t13\t.\t+\t.\tgene_id=ndls0;gene_name=gene0
/// ";
/// let mut reader = gff::Reader::new(&data[..]);
///
/// let mut buf = String::new();
/// reader.read_line(&mut buf)?;
/// assert_eq!(buf, "##gff-version 3");
/// # Ok::<_, io::Error>(())
/// ```
pub fn read_line(&mut self, buf: &mut String) -> io::Result<usize> {
read_line(&mut self.inner, buf)
}
/// Returns an iterator over lines starting from the current stream position.
///
/// When using this, the caller is responsible to stop reading at either EOF or when the
/// `FASTA` directive is read, whichever comes first.
///
/// Unlike [`Self::read_line`], each line is parsed as a [`crate::Line`].
///
/// # Examples
///
/// ```
/// # use std::io;
/// use noodles_gff as gff;
///
/// let data = b"##gff-version 3
/// sq0\tNOODLES\tgene\t8\t13\t.\t+\t.\tgene_id=ndls0;gene_name=gene0
/// ";
/// let mut reader = gff::Reader::new(&data[..]);
/// let mut lines = reader.lines();
///
/// let line = lines.next().transpose()?;
/// assert!(matches!(line, Some(gff::Line::Directive(_))));
///
/// let line = lines.next().transpose()?;
/// assert!(matches!(line, Some(gff::Line::Record(_))));
///
/// assert!(lines.next().is_none());
/// # Ok::<_, io::Error>(())
/// ```
pub fn lines(&mut self) -> Lines<'_, R> {
Lines::new(self)
}
/// Returns an iterator over records starting from the current stream position.
///
/// This filters lines for only records. It stops at either EOF or when the `FASTA` directive
/// is read, whichever comes first.
///
/// # Examples
///
/// ```
/// # use std::io;
/// use noodles_gff as gff;
///
/// let data = b"##gff-version 3
/// sq0\tNOODLES\tgene\t8\t13\t.\t+\t.\tgene_id=ndls0;gene_name=gene0
/// ";
/// let mut reader = gff::Reader::new(&data[..]);
/// let mut records = reader.records();
///
/// assert!(records.next().transpose()?.is_some());
/// assert!(records.next().is_none());
/// # Ok::<_, io::Error>(())
/// ```
pub fn records(&mut self) -> Records<'_, R> {
Records::new(self.lines())
}
}
fn read_line<R>(reader: &mut R, buf: &mut String) -> io::Result<usize>
where
R: BufRead,
{
match reader.read_line(buf) {
Ok(0) => Ok(0),
Ok(n) => {
if buf.ends_with(LINE_FEED) {
buf.pop();
if buf.ends_with(CARRIAGE_RETURN) {
buf.pop();
}
}
Ok(n)
}
Err(e) => Err(e),
}
}
#[cfg(test)]
mod tests {
use super::*;
#[test]
fn test_records() -> io::Result<()> {
let data = b"\
##gff-version 3
sq0\tNOODLES\tgene\t8\t13\t.\t+\t.\tgene_id=ndls0;gene_name=gene0
";
let mut reader = Reader::new(&data[..]);
let mut n = 0;
for result in reader.records() {
let _ = result?;
n += 1;
}
assert_eq!(n, 1);
Ok(())
}
#[test]
fn test_records_with_fasta_directive() -> io::Result<()> {
let data = b"\
##gff-version 3
sq0\tNOODLES\tgene\t8\t13\t.\t+\t.\tgene_id=ndls0;gene_name=gene0
##FASTA
>sq0
ACGT
";
let mut reader = Reader::new(&data[..]);
let mut n = 0;
for result in reader.records() {
let _ = result?;
n += 1;
}
assert_eq!(n, 1);
Ok(())
}
#[test]
fn test_read_line() -> io::Result<()> {
let mut buf = String::new();
let data = b"noodles\n";
let mut reader = &data[..];
read_line(&mut reader, &mut buf)?;
assert_eq!(buf, "noodles");
let data = b"noodles\r\n";
let mut reader = &data[..];
buf.clear();
read_line(&mut reader, &mut buf)?;
assert_eq!(buf, "noodles");
let data = b"noodles";
let mut reader = &data[..];
buf.clear();
read_line(&mut reader, &mut buf)?;
assert_eq!(buf, "noodles");
Ok(())
}
}