Merge pull request #3 from vsbuffalo/new-io

New csv + serde parsing, with cleaner type inference; new `TsvRecordI…

Cargo.toml

@@ -27,7 +27,8 @@ bytes = "1.5.0"
 ndarray-npy = { version = "0.8.1", optional = true }
 num-traits = "0.2.18"
 lazy_static = "1.4.0"
-medians = "3.0.6"
+csv = "1.3.0"
+serde = { version = "1.0.197", features = ["derive"] }
 
 [features]
 # cli = [ "clap" ] # TODO make feature
@@ -54,3 +55,7 @@ criterion = { version = "0.5.1", features = ["html_reports"] }
 name = "bedtools_comparison"
 harness = false
 
+[[bench]]
+name = "io"
+harness = false
+

README.md

@@ -36,7 +36,7 @@ let results_gr = left_gr
  // Find overlaps
  .left_overlaps(&right_gr)?
  // Summarize overlap data
- .map_over_joins(mean_score)?;
+ .map_joins(mean_score)?;
 ```
 
 where `mean_score()` is:

benches/io.rs

@@ -0,0 +1,66 @@
+use criterion::{criterion_group, criterion_main, Criterion};
+use csv::{self, ReaderBuilder};
+use granges::io::parsers::Bed5Addition;
+use granges::ranges::GenomicRangeRecord;
+use granges::test_utilities::random_bed5file;
+use granges::{prelude::*, Position};
+
+#[derive(Debug, serde::Deserialize, PartialEq)]
+struct Bed5Row {
+ seqname: String,
+ start: Position,
+ end: Position,
+ name: String,
+ score: f64,
+}
+
+const BED_LENGTH: usize = 1_000_000;
+
+fn bench_io_shootout(c: &mut Criterion) {
+ // create the benchmark group
+ let mut group = c.benchmark_group("adjust");
+
+ // create the test data
+ let input_bedfile = random_bed5file(BED_LENGTH);
+
+ let genome = read_seqlens("tests_data/hg38_seqlens.tsv").unwrap();
+
+ // configure the sample size for the group
+ group.sample_size(10);
+
+ // Bed5Iterator
+ group.bench_function("bed5iterator", |b| {
+ b.iter(|| {
+ let iter = Bed5Iterator::new(input_bedfile.path()).unwrap();
+ let gr = GRanges::from_iter(iter, &genome).unwrap();
+ gr.len()
+ });
+ });
+
+ // CSV
+ group.bench_function("csv", |b| {
+ b.iter(|| {
+ let mut rdr = ReaderBuilder::new()
+ .delimiter(b'\t')
+ .has_headers(false)
+ .from_path(input_bedfile.path())
+ .unwrap();
+
+ let iter = rdr.deserialize();
+ let mut gr: GRanges<VecRangesIndexed, Vec<Bed5Addition>> = GRanges::new_vec(&genome);
+
+ for result in iter {
+ let row: GenomicRangeRecord<Bed5Addition> = result.unwrap();
+ let data = Bed5Addition {
+ name: row.data.name,
+ score: row.data.score,
+ };
+ gr.push_range(&row.seqname, row.start, row.end, data)
+ .unwrap();
+ }
+ });
+ });
+}
+
+criterion_group!(benches, bench_io_shootout,);
+criterion_main!(benches);

examples/mean_score.rs

@@ -1,18 +1,20 @@
-use granges::{prelude::*, join::CombinedJoinDataLeftEmpty};
+use granges::{join::CombinedJoinDataLeftEmpty, prelude::*};
 
 // Our overlap data processing function.
 pub fn mean_score(join_data: CombinedJoinDataLeftEmpty<Option<f64>>) -> f64 {
  // Get the "right data" -- the BED5 scores.
- let overlap_scores: Vec<f64> = join_data.right_data.into_iter()
+ let overlap_scores: Vec<f64> = join_data
+ .right_data
+ .into_iter()
  // filter out missing values ('.' in BED)
- .filter_map(|x| x).collect();
+ .filter_map(|x| x)
+ .collect();
 
  // calculate the mean
  let score_sum: f64 = overlap_scores.iter().sum();
  score_sum / (overlap_scores.len() as f64)
 }
 
-
 fn try_main() -> Result<(), granges::error::GRangesError> {
  // Mock sequence lengths (e.g. "genome" file)
  let genome = seqlens!("chr1" => 100, "chr2" => 100);
@@ -30,18 +32,17 @@ fn try_main() -> Result<(), granges::error::GRangesError> {
  // Convert to interval trees.
  .into_coitrees()?
  // Extract out just the score from the additional BED5 columns.
- .map_data(|bed5_cols| {
- bed5_cols.score
- })?;
+ .map_data(|bed5_cols| bed5_cols.score)?;
 
  // Compute overlaps and combine scores into mean.
  let results_gr = left_gr
  .left_overlaps(&right_gr)?
- .map_over_joins(mean_score)?;
+ .map_joins(mean_score)?;
 
  results_gr.to_tsv(None::<String>, &BED_TSV)?;
  Ok(())
 }
 
-fn main() { try_main().unwrap(); }
-
+fn main() {
+ try_main().unwrap();
+}

src/commands.rs

@@ -453,7 +453,7 @@ pub fn granges_map(
  let left_join_gr = left_gr.left_overlaps(&right_gr)?;
 
  // Process all the overlaps.
- let result_gr = left_join_gr.map_over_joins(|join_data| {
+ let result_gr = left_join_gr.map_joins(|join_data| {
  // Get the "right data" -- the BED5 scores
  let mut overlap_scores: Vec<f64> = join_data
  .right_data

src/data/operations.rs

@@ -20,8 +20,8 @@ pub fn median<F: Float + Sum>(numbers: &mut [F]) -> Option<F> {
  }
  let mid = numbers.len() / 2;
  if numbers.len() % 2 == 0 {
- numbers.select_nth_unstable_by(mid-1, |a, b| a.partial_cmp(b).unwrap());
- let lower = numbers[mid-1];
+ numbers.select_nth_unstable_by(mid - 1, |a, b| a.partial_cmp(b).unwrap());
+ let lower = numbers[mid - 1];
  numbers.select_nth_unstable_by(mid, |a, b| a.partial_cmp(b).unwrap());
  let upper = numbers[mid];
  Some((lower + upper) / F::from(2.0).unwrap())
@@ -93,7 +93,7 @@ impl Operation {
 
 #[cfg(test)]
 mod tests {
-  use super::*;
+ use super::*;
 
  #[test]
  fn test_median_empty() {
@@ -118,5 +118,4 @@ mod tests {
  let mut numbers = vec![-3.0, -1.0, -2.0];
  assert_eq!(median(&mut numbers), Some(-2.0));
  }
-
 }

src/error.rs

@@ -75,6 +75,9 @@ pub enum GRangesError {
  #[error("File reading error: {0}. Please check if the file exists and you have permission to read it.")]
  IOError(#[from] std::io::Error),
 
+ #[error("File parsing error: {0}")]
+ TsvParsingError(#[from] csv::Error),
+
  // File parsing related errors
  #[error("Could not determine the file type based on its extension. Ensure the file has a standard genomic data extension (.bed, .gff, etc.).")]
  CouldNotDetectRangesFiletype,

src/granges.rs

@@ -806,7 +806,7 @@ where
  /// See [`CombinedJoinData`] and its convenience methods, which are designed
  /// to help downstream statistical calculations that could use the number of overlapping
  /// basepairs, overlapping fraction, etc.
- pub fn map_over_joins<F, V>(
+ pub fn map_joins<F, V>(
  mut self,
  func: F,
  ) -> Result<GRanges<VecRangesIndexed, Vec<V>>, GRangesError>
@@ -847,7 +847,7 @@ impl GRanges<VecRangesIndexed, JoinDataBothEmpty> {
  /// to help downstream statistical calculations that could use the number of overlapping
  /// basepairs, overlapping fraction, etc.
 
- pub fn map_over_joins<F, V>(
+ pub fn map_joins<F, V>(
  mut self,
  func: F,
  ) -> Result<GRanges<VecRangesIndexed, Vec<V>>, GRangesError>
@@ -885,7 +885,7 @@ where
  /// See [`CombinedJoinDataRightEmpty`] and its convenience methods, which are designed
  /// to help downstream statistical calculations that could use the number of overlapping
  /// basepairs, overlapping fraction, etc.
- pub fn map_over_joins<F, V>(
+ pub fn map_joins<F, V>(
  mut self,
  func: F,
  ) -> Result<GRanges<VecRangesIndexed, Vec<V>>, GRangesError>
@@ -924,7 +924,7 @@ where
  /// to help downstream statistical calculations that could use the number of overlapping
  /// basepairs, overlapping fraction, etc.
 
- pub fn map_over_joins<F, V>(
+ pub fn map_joins<F, V>(
  mut self,
  func: F,
  ) -> Result<GRanges<VecRangesIndexed, Vec<V>>, GRangesError>
@@ -1470,7 +1470,7 @@ mod tests {
  }
 
  #[test]
- fn test_map_over_joins() {
+ fn test_map_oins() {
  let sl = seqlens!("chr1" => 50);
  let windows: GRangesEmpty<VecRangesEmpty> =
  GRangesEmpty::from_windows(&sl, 10, None, true).unwrap();
@@ -1487,7 +1487,7 @@ mod tests {
  let joined_results = windows
  .left_overlaps(&right_gr)
  .unwrap()
- .map_over_joins(|join_data| {
+ .map_joins(|join_data| {
  let overlap_scores = join_data.right_data;
  overlap_scores.iter().sum::<f64>()
  })

src/io/mod.rs

@@ -6,7 +6,7 @@ pub mod tsv;
 
 pub use file::{InputStream, OutputStream};
 pub use parsers::{
- Bed3Iterator, Bed5Iterator, BedlikeIterator, GenomicRangesFile, GenomicRangesParser,
- TsvRecordIterator,
+ bed::Bed3Iterator, bed::Bed5Iterator, bed::BedlikeIterator, tsv::TsvRecordIterator,
+ GenomicRangesFile, GenomicRangesParser,
 };
 pub use tsv::BED_TSV;