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// Copyright (C) 2024 Philipp Benner
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the “Software”), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
// SOFTWARE.
use std::fs::File;
use std::io::{self, Read, Seek};
use crate::bigwig::BigWigReader;
use crate::granges::GRanges;
use crate::meta::MetaData;
use crate::track_statistics::BinSummaryStatistics;
/* -------------------------------------------------------------------------- */
impl GRanges {
pub fn read_bigwig<R: Read + Seek>(
&mut self,
reader: &mut R,
name: &str,
f: BinSummaryStatistics,
mut bin_size: usize,
bin_overlap: usize,
init: f64,
rev_neg_strand: bool,
) -> Result<(), Box<dyn std::error::Error>> {
let mut bwr = BigWigReader::new(reader)?;
let mut counts = Vec::with_capacity(self.num_rows());
for i in 0..self.num_rows() {
let (mut values, detected_bin_size) = bwr.query_slice(
&self.seqnames[i],
self.ranges[i].from,
self.ranges[i].to,
f,
bin_size,
bin_overlap,
init,
)?;
if bin_size == 0 {
bin_size = detected_bin_size;
}
if rev_neg_strand && self.strand[i] == '-' {
values.reverse();
}
counts.push(values);
}
self.meta.delete_meta(name);
self.meta.add(name, MetaData::FloatMatrix(counts))?;
Ok(())
}
pub fn import_bigwig(
&mut self,
filename: &str,
name: &str,
f: BinSummaryStatistics,
bin_size: usize,
bin_overlap: usize,
init: f64,
rev_neg_strand: bool,
) -> Result<(), Box<dyn std::error::Error>> {
let mut file = File::open(filename)?;
self.read_bigwig(
&mut file,
name,
f,
bin_size,
bin_overlap,
init,
rev_neg_strand,
)
.map_err(|e| {
Box::new(io::Error::new(
io::ErrorKind::Other,
format!("importing bigWig file from `{}` failed: {}", filename, e),
)) as Box<dyn std::error::Error>
})
}
}
/* -------------------------------------------------------------------------- */
#[cfg(test)]
mod tests {
use crate::granges::GRanges;
use crate::meta::MetaData;
use crate::track_statistics::bin_summary_statistics_from_string;
#[test]
fn granges_import_bigwig_reads_values_into_float_matrix() {
let mut granges = GRanges::new(
vec!["chrY".into(), "chrY".into()],
vec![1838100, 1838100],
vec![1838600, 1838300],
vec!['+', '-'],
);
granges
.import_bigwig(
"tests/test_bigwig_2.bw",
"signal",
bin_summary_statistics_from_string("mean").unwrap(),
100,
0,
0.0,
true,
)
.unwrap();
match granges.meta.get_column("signal").unwrap() {
MetaData::FloatMatrix(v) => {
assert_eq!(v[0], vec![1.0, 1.0, 0.0, 0.0, 0.0]);
assert_eq!(v[1], vec![1.0, 1.0]);
}
_ => panic!("expected FloatMatrix"),
}
}
}