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Cargo.toml

@@ -0,0 +1,20 @@
+[package]
+name = "rnaseq_features_counter"
+version = "0.1.0"
+edition = "2021"
+
+[dependencies]
+anyhow = "1.0.93"
+bio-types = "1.0.4"
+clap = { version = "4.5.21", features = ["derive"] }
+dashmap = { version = "6.1.0", features = ["rayon"] }
+env_logger = "0.11.5"
+log = "0.4.22"
+noodles-bgzf = "0.33.0"
+noodles-core = "0.15.0"
+noodles-gff = "0.39.0"
+noodles-vcf = "0.68.0"
+rayon = "1.10.0"
+rust-htslib = "0.48.0"
+statrs = "0.17.1"
+

src/main.rs

@@ -0,0 +1,598 @@
+use anyhow::Context;
+
+use dashmap::DashMap;
+use noodles_bgzf as bgzf;
+use noodles_core::{Position, Region};
+use noodles_gff as gff;
+use noodles_vcf::{self as vcf};
+use rust_htslib::{bam, bam::Read};
+
+use clap::Parser;
+use log::info;
+use statrs::distribution::{ChiSquared, ContinuousCDF};
+use std::{
+    collections::HashMap,
+    fmt,
+    fs::File,
+    io::{BufReader, Write},
+    time::Instant,
+};
+
+use rayon::prelude::*;
+
+#[derive(Parser, Debug)]
+#[command(author, version, about, long_about = None)]
+struct Args {
+    #[arg(short = 'b', long)]
+    bam_path: String,
+
+    #[arg(short = 'v', long)]
+    constit_vcf: String,
+
+    #[arg(short, long)]
+    gff_path: String,
+
+    #[arg(short, long)]
+    out_prefix: String,
+}
+
+#[derive(Debug, Default, Clone)]
+struct Exon {
+    id: String,
+    contig: String,
+    start: u32, // inclusive 1-based inclusive
+    end: u32,
+    strand: noodles_gff::record::Strand,
+    depth_start: u32,
+    depth_before_start: u32,
+    depth_end: u32,
+    depth_after_end: u32,
+    mean_depth: u32,
+    snps: Vec<Snp>,
+}
+
+impl fmt::Display for Exon {
+    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
+        let n_p_sign = self
+            .snps
+            .iter()
+            .filter_map(|s| s.get_p().ok())
+            .filter(|p| p <= &0.01)
+            .count();
+
+        writeln!(
+            f,
+            "{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}",
+            self.contig,
+            self.start,
+            self.end,
+            self.mean_depth,
+            n_p_sign,
+            self.depth_before_start,
+            self.depth_start,
+            self.depth_end,
+            self.depth_after_end,
+            self.id
+        )
+    }
+}
+
+// impl FromStr for Exon {
+//     type Err = anyhow::Error;
+//
+//     fn from_str(s: &str) -> anyhow::Result<Self> {
+//         let parts: Vec<&str> = s.split('-').collect();
+//         if parts.len() != 2 {
+//             return Err("Invalid format".parse().unwrap());
+//         }
+//
+//         let start = parts[0].parse()?;
+//         let end = parts[1].parse()?;
+//
+//         Ok(Exon {})
+//     }
+// }
+
+#[derive(Debug, Clone)]
+struct Snp {
+    pos: u32,
+    alt: u8,
+    n_alt_mrd: u32,
+    depth_mrd: u32,
+    n_alt_rna: Option<u32>,
+    depth_rna: Option<u32>,
+}
+
+fn main() -> anyhow::Result<()> {
+    let now = Instant::now();
+    env_logger::init();
+
+    let args = Args::parse();
+
+    // let mut vcf_reader = vcf::io::indexed_reader::Builder::default()
+    //     .build_from_path(&args.constit_vcf)
+    //     .context(format!("Failed to open: {}", args.constit_vcf))?;
+    // let header = vcf_reader.read_header()?;
+
+    // let mut gff_reader = File::open(&args.gff_path)
+    //     .map(BufReader::new)
+    //     .context(format!("Failed to open: {}", args.gff_path))?;
+    //
+    // let mut buffer = [0u8; 1];
+    // let mut line_buffer = Vec::new();
+    //
+    // let mut exons: Vec<Exon> = Vec::new();
+    // loop {
+    //     match std::io::Read::read_exact(&mut gff_reader, &mut buffer) {
+    //         Ok(_) => {
+    //             // Process each byte here
+    //             println!("Byte: {}", buffer[0]);
+    //             match buffer[0] {
+    //                 b'\n' => {
+    //                     // new line
+    //                     let line_str = str::from_utf8(&line_buffer)?;
+    //                     line_buffer.clear();
+    //                     if line_str.contains("\texon\t") {
+    //                         exons.push(line_str.parse()?);
+    //                     }
+    //                 }
+    //                 _ => {
+    //                     line_buffer.push(buffer[0]);
+    //                 }
+    //             }
+    //         }
+    //         Err(e) if e.kind() == std::io::ErrorKind::UnexpectedEof => {
+    //             // Reached end of file
+    //             break;
+    //         }
+    //         Err(e) => anyhow::bail!(e),
+    //     }
+    // }
+
+    let mut gff_reader = File::open(&args.gff_path)
+        .map(BufReader::new)
+        .map(gff::io::Reader::new)
+        .context(format!("Failed to open: {}", args.gff_path))?;
+
+    let out_exons = format!("{}_exons.gz", args.out_prefix);
+    let out_genes = format!("{}_genes.gz", args.out_prefix);
+
+    let mut n_exons = 0;
+    let mut exons: Vec<Exon> = Vec::new();
+    for result in gff_reader.records() {
+        let record = result?;
+
+        if record.ty() == "exon" {
+            let mut exon = Exon::default();
+            let ids: Vec<String> = record
+                .attributes()
+                .iter()
+                .filter(|(k, _)| *k == "Parent")
+                .filter_map(|(_, v)| {
+                    if let noodles_gff::record::attributes::field::value::Value::String(s) = v {
+                        Some(s.to_string())
+                    } else {
+                        None
+                    }
+                })
+                .collect();
+            exon.id = ids
+                .first()
+                .map(|s| s.as_str())
+                .unwrap_or("No_id")
+                .to_string();
+            if !exon.id.starts_with("NM") {
+                continue;
+            }
+            let contig = record.reference_sequence_name();
+            exon.contig = contig.to_string();
+            let gff_start = record.start(); // [1]
+            exon.start = gff_start.get() as u32;
+            let gff_end = record.end();
+            exon.end = gff_end.get() as u32;
+            // let region = Region::new(contig, gff_start..=gff_end);
+            let gff_strand = record.strand();
+            exon.strand = gff_strand;
+
+            // let query = vcf_reader.query(&header, &region)?;
+            // let mut snps = Vec::new();
+            // for result in query {
+            //     let record = Snp::from_vcf_record(&result?, &header)?;
+            //     snps.push(record);
+            // }
+
+            // exon.snps = snps;
+
+            exons.push(exon);
+            n_exons += 1;
+
+            if n_exons % 10_000 == 0 {
+                info!("{n_exons} exons parsed.");
+            }
+        }
+    }
+
+    info!(
+        "{} exons to look in bam file in {} chunks...",
+        exons.len(),
+        exons.len() / 1_000
+    );
+
+    let contig_exons: DashMap<String, Vec<Exon>> = DashMap::new();
+    exons.par_chunks(1_000).enumerate().for_each(|(nc, c)| {
+        let mut bam_reader = bam::IndexedReader::from_path(&args.bam_path)
+            .context(format!("Failed to open: {}", args.bam_path))
+            .unwrap();
+
+        let mut vcf_reader = vcf::io::indexed_reader::Builder::default()
+            .build_from_path(&args.constit_vcf)
+            .context(format!("Failed to open: {}", args.constit_vcf))
+            .unwrap();
+        let header = vcf_reader.read_header().unwrap();
+
+        for exon in c {
+            let mut exon = exon.clone();
+
+            let start = Position::try_from(exon.start as usize).unwrap();
+            let end = Position::try_from(exon.end as usize).unwrap();
+            let region = Region::new(exon.contig.clone(), start..=end);
+            let query = vcf_reader.query(&header, &region).unwrap();
+            for result in query {
+                let record = Snp::from_vcf_record(&result.unwrap(), &header).unwrap();
+                exon.snps.push(record);
+            }
+
+            let bam_start = exon.start - 1; // [0] <- bug ??
+            let bam_end = exon.end - 1;
+            bam_reader
+                .fetch((&exon.contig, bam_start, bam_end))
+                .unwrap();
+
+            let mut len = 0;
+            let mut depths = 0;
+
+            let snps_pos: Vec<u32> = exon.snps.iter().map(|s| s.pos).collect();
+            for p in bam_reader.pileup() {
+                let pile = p.unwrap();
+                let pos = pile.pos();
+
+                let mut depth = 0;
+                let mut bases = Vec::new();
+                let populate_bases = snps_pos.contains(&pos);
+                for a in pile.alignments() {
+                    if a.is_refskip() || a.is_del() {
+                        continue;
+                    }
+                    let r = a.record();
+
+                    match (r.strand(), exon.strand) {
+                        // dont ask me why it's inverted.....
+                        (
+                            bio_types::strand::ReqStrand::Reverse,
+                            noodles_gff::record::Strand::Forward,
+                        ) => depth += 1,
+                        (
+                            bio_types::strand::ReqStrand::Forward,
+                            noodles_gff::record::Strand::Reverse,
+                        ) => depth += 1,
+                        _ => (),
+                    }
+
+                    if populate_bases {
+                        match a.indel() {
+                            bam::pileup::Indel::Ins(_len) => bases.push(b'I'),
+                            bam::pileup::Indel::Del(_len) => bases.push(b'D'),
+                            _ => {
+                                if r.seq_len() > 0 {
+                                    if let Some(b) = hts_base_at(&r, pos, false).unwrap() {
+                                        bases.push(b);
+                                    }
+                                } else if a.is_del() {
+                                    bases.push(b'D');
+                                }
+                            }
+                        }
+                    }
+                }
+
+                // one before start and one after end
+                if pos == bam_start - 1 {
+                    exon.depth_before_start = depth;
+                }
+
+                if pos == bam_start {
+                    exon.depth_start = depth;
+                }
+
+                if pos == bam_end {
+                    exon.depth_end = depth;
+                }
+
+                if pos == bam_end + 1 {
+                    exon.depth_after_end = depth;
+                }
+
+                // for mean depth
+                if pos >= bam_start && pos <= bam_end {
+                    len += 1;
+                    depths += depth;
+                }
+
+                if populate_bases {
+                    exon.snps.iter_mut().filter(|s| s.pos == pos).for_each(|s| {
+                        s.n_alt_rna = Some(bases.iter().filter(|b| **b == s.alt).count() as u32);
+                        s.depth_rna = Some(bases.len() as u32);
+                    });
+                }
+            }
+
+            exon.mean_depth = (depths as f64 / len as f64).round() as u32;
+            contig_exons
+                .entry(exon.contig.clone())
+                .or_default()
+                .push(exon);
+        }
+        info!("chunk {nc} finished.");
+    });
+
+    let bam_reader = bam::IndexedReader::from_path(&args.bam_path)
+        .context(format!("Failed to open: {}", args.bam_path))
+        .unwrap();
+    let contigs: Vec<String> = bam_reader
+        .header()
+        .target_names()
+        .iter()
+        .map(|s| String::from_utf8(s.to_vec()).unwrap())
+        .collect();
+
+    let mut genes: HashMap<String, (String, u32, Vec<u32>)> = HashMap::new();
+    let mut writer = File::create(out_exons).map(bgzf::MultithreadedWriter::new)?;
+    contigs.iter().for_each(|c| {
+        if let Some(exons) = contig_exons.get(c) {
+            let mut exons = exons.clone();
+            info!("Sorting {c}");
+            exons.par_sort_by(|a, b| a.start.cmp(&b.start));
+            info!("Writing {c}");
+            exons.iter().for_each(|e| {
+                writer.write_all(e.to_string().as_bytes()).unwrap();
+                genes
+                    .entry(e.id.clone())
+                    .or_insert((e.id.clone(), e.start, Vec::new()))
+                    .2
+                    .push(e.mean_depth);
+                writer.flush().unwrap();
+            });
+        }
+    });
+
+    writer.finish()?;
+    let genes: Vec<_> = genes
+        .values()
+        .map(|(c, p, v)| {
+            let sum: u32 = v.iter().copied().sum();
+            (c.to_string(), *p, sum as f64 / v.len() as f64)
+        })
+        .collect();
+
+    let mut writer = File::create(out_genes).map(bgzf::MultithreadedWriter::new)?;
+    contigs.iter().for_each(|c| {
+        let mut g: Vec<&(String, u32, f64)> =
+            genes.iter().filter(|(contig, _, _)| c == contig).collect();
+
+        info!("Sorting {c}");
+        g.par_sort_by(|a, b| a.1.cmp(&b.1));
+        info!("Writing {c}");
+        g.iter().for_each(|e| {
+            writer
+                .write_all(
+                    [e.0.to_string(), e.1.to_string(), e.2.to_string()]
+                        .join("\t")
+                        .as_bytes(),
+                )
+                .unwrap();
+            writer.flush().unwrap();
+        });
+    });
+    writer.finish()?;
+
+
+    info!("Process done in {:#?}", now.elapsed());
+    Ok(())
+}
+
+impl Snp {
+    pub fn from_vcf_record(
+        value: &noodles_vcf::record::Record,
+        header: &noodles_vcf::Header,
+    ) -> anyhow::Result<Self> {
+        let pos = value
+            .variant_start()
+            .context(format!("Can't parse variant start {:?}", value))?
+            .context(format!("Can't parse variant start {:?}", value))?
+            .get() as u32;
+        let alt = *value
+            .alternate_bases()
+            .as_ref()
+            .as_bytes()
+            .to_vec()
+            .first()
+            .context(format!("Can't parse variant alt {:?}", value))?;
+        let (dp, ad) = get_dp_ad(value, header)?;
+
+        Ok(Snp {
+            pos,
+            alt,
+            n_alt_mrd: ad[1],
+            depth_mrd: dp,
+            n_alt_rna: None,
+            depth_rna: None,
+        })
+    }
+
+    pub fn get_p(&self) -> anyhow::Result<f64> {
+        let depth_rna = self.depth_rna.context("")?;
+        let n_alt_rna = self.n_alt_rna.context("")?;
+        // Homozygote SNP
+        if self.n_alt_mrd == self.depth_mrd {
+            if depth_rna > 6 && n_alt_rna == 0 {
+                return Ok(0.0);
+            } else if n_alt_rna == depth_rna {
+                return Ok(1.0);
+            }
+        }
+        chi_square_test_for_proportions(
+            self.n_alt_mrd as f64,
+            self.depth_mrd as f64,
+            self.n_alt_rna.context("")? as f64,
+            self.depth_rna.context("")? as f64,
+        )
+    }
+}
+
+pub fn get_dp_ad(
+    record: &noodles_vcf::record::Record,
+    header: &noodles_vcf::Header,
+) -> anyhow::Result<(u32, Vec<u32>)> {
+    Ok((record.samples().iter().next().and_then(|s| {
+        s.iter(header).find_map(|g| {
+            g.ok().and_then(|(k, v)| {
+                if k == "DP" {
+                    v.and_then(|v| match v {
+                        noodles_vcf::variant::record::samples::series::Value::Integer(i) => Some(i as u32),
+                        _ => None
+                    })
+                } else {
+                    None
+                }
+            })
+        })
+    }).context(format!("Error while parsing AD {:?}", record))?,
+    record
+        .samples()
+        .iter()
+        .next()
+        .and_then(|s| {
+            s.iter(header)
+                .find_map(|g| {
+                    g.ok().and_then(|(k, v)| {
+                        if k == "AD" {
+                            v.and_then(|v| match v {
+                                noodles_vcf::variant::record::samples::series::Value::Array(noodles_vcf::variant::record::samples::series::value::Array::Integer(values)) => Some(values),
+                                _ => None,
+                            })
+                        } else {
+                            None
+                        }
+                    })
+                })
+        })
+        .map(|values| {
+            values
+                .iter()
+                .filter_map(|v| v.ok().and_then(|v| v.map(|i| i as u32)))
+                .collect()
+        })
+        .context(format!("Error while parsing AD {:?}", record))?))
+}
+
+pub fn hts_base_at(
+    record: &rust_htslib::bam::record::Record,
+    at_pos: u32,
+    with_next_ins: bool,
+) -> anyhow::Result<Option<u8>> {
+    use rust_htslib::bam::record::Cigar;
+
+    let cigar = record.cigar();
+    let seq = record.seq();
+    let pos = cigar.pos() as u32;
+
+    let mut read_i = 0u32;
+    let at_pos = at_pos - 1;
+    let mut ref_pos = pos;
+    if ref_pos > at_pos {
+        return Ok(None);
+    }
+
+    for (id, op) in cigar.iter().enumerate() {
+        let (add_read, add_ref) = match *op {
+            Cigar::Match(len) | Cigar::Equal(len) | Cigar::Diff(len) => (len, len),
+            Cigar::Ins(len) => (len, 0),
+            Cigar::Del(len) => (0, len),
+            Cigar::RefSkip(len) => (0, len),
+            Cigar::SoftClip(len) => (len, 0),
+            Cigar::HardClip(_) | Cigar::Pad(_) => (0, 0),
+        };
+        // If at the end of the op len and next op is Ins return I
+        if with_next_ins && ref_pos + add_read == at_pos + 1 {
+            if let Some(Cigar::Ins(_)) = cigar.get(id + 1) {
+                return Ok(Some(b'I'));
+            }
+        }
+
+        if ref_pos + add_ref > at_pos {
+            // Handle deletions directly
+            if let Cigar::Del(_) = *op {
+                return Ok(Some(b'D'));
+            } else if let Cigar::RefSkip(_) = op {
+                return Ok(None);
+            } else {
+                let diff = at_pos - ref_pos;
+                let p = read_i + diff;
+                return Ok(Some(seq[p as usize]));
+            }
+        }
+
+        read_i += add_read;
+        ref_pos += add_ref;
+    }
+    Ok(None)
+}
+
+pub fn chi_square_test_impl(observed: &[f64], expected: &[f64]) -> anyhow::Result<f64> {
+    if observed.len() != expected.len() {
+        return Err(anyhow::anyhow!("Input vectors must have the same length"));
+    }
+
+    // Calculate the chi-squared statistic
+    let chi_squared_statistic: f64 = observed
+        .iter()
+        .zip(expected.iter())
+        .map(|(obs, exp)| ((obs - exp).abs() - 0.5).powi(2) / exp)
+        .sum();
+
+    // Degrees of freedom is the number of categories minus 1
+    // let degrees_of_freedom = (observed.len() - 1) as f64;
+    let degrees_of_freedom = 1.0;
+
+    // Calculate p-value using chi-squared distribution
+    let chi_squared_distribution = ChiSquared::new(degrees_of_freedom).unwrap();
+    let p_value = 1.0 - chi_squared_distribution.cdf(chi_squared_statistic);
+
+    // You can use the p-value to make decisions based on your significance level
+    // For example, with a significance level of 0.05, if p_value < 0.05, reject the null hypothesis
+    Ok(p_value)
+}
+
+/// 2-sample test for equality of proportions with continuity correction
+/// remerciements to chatGPT
+pub fn chi_square_test_for_proportions(
+    success_a: f64,
+    total_a: f64,
+    success_b: f64,
+    total_b: f64,
+) -> anyhow::Result<f64> {
+    let observed_counts = vec![
+        success_a,
+        total_a - success_a,
+        success_b,
+        total_b - success_b,
+    ];
+    let expected_counts = vec![
+        total_a * (success_a + success_b) / (total_a + total_b),
+        total_a * (total_a - success_a + total_b - success_b) / (total_a + total_b),
+        total_b * (success_a + success_b) / (total_a + total_b),
+        total_b * (total_a - success_a + total_b - success_b) / (total_a + total_b),
+    ];
+
+    chi_square_test_impl(&observed_counts, &expected_counts)
+}