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rsbio_seq-0.1.0/Cargo.toml

@@ -0,0 +1,14 @@
+[package]
+name = "rsbio-seq"
+version = "0.1.0"
+edition = "2021"
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+[lib]
+name = "rsbio_seq"
+crate-type = ["cdylib"]
+
+[dependencies]
+bio = "2.0.1"
+flate2 = "1.0.33"
+pyo3 = { version = "0.22.0", features = ["abi3-py39"] }

rsbio_seq-0.1.0/PKG-INFO

@@ -0,0 +1,7 @@
+Metadata-Version: 2.3
+Name: rsbio-seq
+Version: 0.1.0
+Classifier: Programming Language :: Rust
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+Requires-Python: >=3.9

rsbio_seq-0.1.0/pyproject.toml

@@ -0,0 +1,16 @@
+[build-system]
+requires = ["maturin>=1.7,<2.0"]
+build-backend = "maturin"
+
+[project]
+name = "rsbio-seq"
+requires-python = ">=3.9"
+classifiers = [
+    "Programming Language :: Rust",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Programming Language :: Python :: Implementation :: PyPy",
+]
+dynamic = ["version", "readme", "description", "license", "authors"]
+
+[tool.maturin]
+features = ["pyo3/extension-module"]

rsbio_seq-0.1.0/rsbio_seq.pyi

@@ -0,0 +1,42 @@
+from typing import Iterator
+
+class Sequence:
+    """
+    Sequence entry.
+
+    Attributes
+        id (str): record id of the sequence.
+        desc (str): description of the record if available.
+        seq (str): content of the sequence.
+        qual (str): quality string of the sequence if available.
+    """
+
+    id: str
+    desc: str
+    seq: str
+    qual: str
+
+class SeqIO:
+    """
+    Sequence reader.
+    """
+
+    def __init__(self, path: str) -> None:
+        """
+        Initialise the reader with path of the file.
+
+        Args:
+            path (str): The path to file fasta, fastq, fa, fq and compressed formats with gz are supported.
+        """
+        ...
+
+    def __iter__(self) -> Iterator[Sequence]:
+        """
+        Return an iterator of Sequence objects.
+
+        Returns:
+            Iterator[Sequence]: An iterator over sequences in the file.
+        """
+        ...
+
+__all__ = ["Sequence", "SeqIO"]

rsbio_seq-0.1.0/src/lib.rs

@@ -0,0 +1,43 @@
+mod seq;
+use pyo3::prelude::*;
+use seq::{get_reader, SeqFormat, Sequence, Sequences};
+use std::io::Read;
+
+/// Sequence reader
+#[pyclass]
+pub struct SeqIO {
+    records: Sequences<std::io::BufReader<Box<dyn Read + Send + Sync>>>,
+}
+
+#[pymethods]
+impl SeqIO {
+    /// Initialise a sequence reader for a file in some destination
+    #[new]
+    #[pyo3(signature = (path))]
+    pub fn new(path: String) -> Self {
+        let reader = get_reader(&path).unwrap();
+        let format = SeqFormat::get(&path).expect("Unable to detect file format");
+
+        Self {
+            records: Sequences::new(format, reader).unwrap(),
+        }
+    }
+
+    /// Iterator object
+    pub fn __iter__(slf: PyRef<'_, Self>) -> PyRef<'_, Self> {
+        slf
+    }
+
+    /// Iterate through sequences
+    pub fn __next__(mut slf: PyRefMut<'_, Self>) -> Option<Sequence> {
+        slf.records.next()
+    }
+}
+
+/// Sequence reader for rust
+#[pymodule]
+fn rsbio_seq(m: &Bound<'_, PyModule>) -> PyResult<()> {
+    m.add_class::<Sequence>()?;
+    m.add_class::<SeqIO>()?;
+    Ok(())
+}

rsbio_seq-0.1.0/src/seq.rs

@@ -0,0 +1,228 @@
+use bio::io::fasta::{Reader as FastaReader, Records as FastaRecords};
+use bio::io::fastq::{Reader as FastqReader, Records as FastqRecords};
+use pyo3::prelude::*;
+use std::fs::File;
+use std::io::{BufRead, BufReader, Read};
+
+// Record set entries of type R, which implement BufRead trait (stdin/file)
+pub enum RecordSet<R: BufRead> {
+    Fasta(FastaRecords<BufReader<R>>),
+    Fastq(FastqRecords<BufReader<R>>),
+}
+
+/// Sequence entry
+#[pyclass]
+pub struct Sequence {
+    /// sequence id
+    #[pyo3(get, set)]
+    pub id: String,
+    /// sequence description
+    #[pyo3(get, set)]
+    pub desc: String,
+    /// sequence string
+    #[pyo3(get, set)]
+    pub seq: String,
+    /// sequence quality string (for FASTQ)
+    #[pyo3(get, set)]
+    pub qual: String,
+}
+
+#[derive(Debug, Clone, Copy)]
+pub enum SeqFormat {
+    Fasta,
+    Fastq,
+}
+
+impl SeqFormat {
+    pub fn get(path: &str) -> Option<SeqFormat> {
+        let mut path = path;
+        if path.ends_with(".gz") {
+            path = path.trim_end_matches(".gz");
+        }
+        if path.ends_with(".fq") || path.ends_with(".fastq") {
+            return Some(SeqFormat::Fastq);
+        } else if path.ends_with(".fasta") || path.ends_with(".fa") || path.ends_with(".fna") {
+            return Some(SeqFormat::Fasta);
+        }
+        None
+    }
+}
+
+pub struct Sequences<R: BufRead> {
+    pub records: RecordSet<R>,
+}
+
+impl<R: BufRead> Sequences<R> {
+    pub fn new(format: SeqFormat, reader: R) -> Result<Self, String> {
+        match format {
+            SeqFormat::Fastq => {
+                let fastq_reader = FastqReader::new(reader);
+                Ok(Sequences {
+                    records: RecordSet::Fastq(fastq_reader.records()),
+                })
+            }
+            SeqFormat::Fasta => {
+                let fasta_reader = FastaReader::new(reader);
+                Ok(Sequences {
+                    records: RecordSet::Fasta(fasta_reader.records()),
+                })
+            }
+        }
+    }
+}
+
+impl<R: BufRead> Iterator for Sequences<R> {
+    type Item = Sequence;
+
+    fn next(&mut self) -> Option<Self::Item> {
+        // records do not have a common trait to get id and seq, we can create one
+        // but this looks simpler for the time being
+        match self.records {
+            RecordSet::Fastq(ref mut records) => {
+                let next_record = records.next();
+                if let Some(record) = next_record {
+                    let record = record.unwrap();
+                    return Some(Sequence {
+                        id: record.id().to_string(),
+                        desc: record.desc().unwrap_or("").to_string(),
+                        seq: String::from_utf8_lossy(record.seq()).to_string(),
+                        qual: String::from_utf8_lossy(record.qual()).to_string(),
+                    });
+                }
+                None
+            }
+            RecordSet::Fasta(ref mut records) => {
+                let next_record = records.next();
+                if let Some(record) = next_record {
+                    let record = record.unwrap();
+                    return Some(Sequence {
+                        id: record.id().to_string(),
+                        desc: record.desc().unwrap_or("").to_string(),
+                        seq: String::from_utf8_lossy(record.seq()).to_string(),
+                        qual: "".into(),
+                    });
+                }
+                None
+            }
+        }
+    }
+
+    fn count(self) -> usize
+    where
+        Self: Sized,
+    {
+        unimplemented!("Count cannot be performed without always having a rewindable input stream, stdin is not!");
+    }
+}
+
+pub fn get_reader(path: &str) -> Result<BufReader<Box<dyn Read + Sync + Send>>, String> {
+    let is_zip = path.ends_with(".gz");
+    let file = File::open(path).map_err(|_| format!("Unable to open: {}", path))?;
+    if is_zip {
+        let decoder = flate2::read::GzDecoder::new(file);
+        Ok(BufReader::new(Box::new(decoder)))
+    } else {
+        Ok(BufReader::new(Box::new(file)))
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    const PATH_FQ: &str = "test_data/reads.fq";
+    const PATH_FA: &str = "test_data/reads.fa";
+    const PATH_FQ_GZ: &str = "test_data/reads.fq.gz";
+    const PATH_FA_GZ: &str = "test_data/reads.fa.gz";
+
+    #[test]
+    fn load_fq_file_test() {
+        let reader = get_reader(PATH_FQ).unwrap();
+        let mut seqs = Sequences::new(SeqFormat::Fastq, reader).unwrap();
+        let record_1 = seqs.next().unwrap();
+        assert_eq!("Read_1", record_1.id);
+        assert_eq!(
+            "GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACCAAGTTACCCTTAACAACTTAAGGGTTTTCAAATAGA",
+            record_1.seq
+        );
+        let record_2 = seqs.next().unwrap();
+        assert_eq!("Read_2", record_2.id);
+        assert_eq!(
+            "GTTCAGGGATACGACGTTTGTATTTTAAGAATCTGAAGCAGAAGTCGATGATAATACGCGTCGTTTTATCAT",
+            record_2.seq
+        );
+        let finish = seqs.next();
+        assert!(finish.is_none());
+    }
+
+    #[test]
+    fn load_fq_gz_file_test() {
+        let reader = get_reader(PATH_FQ_GZ).unwrap();
+        let mut seqs = Sequences::new(SeqFormat::Fastq, reader).unwrap();
+        let record_1 = seqs.next().unwrap();
+        assert_eq!("Read_1", record_1.id);
+        assert_eq!(
+            "GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACCAAGTTACCCTTAACAACTTAAGGGTTTTCAAATAGA",
+            record_1.seq
+        );
+        let record_2 = seqs.next().unwrap();
+        assert_eq!("Read_2", record_2.id);
+        assert_eq!(
+            "GTTCAGGGATACGACGTTTGTATTTTAAGAATCTGAAGCAGAAGTCGATGATAATACGCGTCGTTTTATCAT",
+            record_2.seq
+        );
+        let finish = seqs.next();
+        assert!(finish.is_none());
+    }
+
+    #[test]
+    fn load_fa_file_test() {
+        let reader = get_reader(PATH_FA).unwrap();
+        let mut seqs = Sequences::new(SeqFormat::Fasta, reader).unwrap();
+        let record_1 = seqs.next().unwrap();
+        assert_eq!("Record_1", record_1.id);
+        assert_eq!(
+            "GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACCAAGTTACCCTTAACAACTTAAGGGTTTTCAAATAGA",
+            record_1.seq
+        );
+        let record_2 = seqs.next().unwrap();
+        assert_eq!("Record_2", record_2.id);
+        assert_eq!(
+            "GTTCAGGGATACGACGTTTGTATTTTAAGAATCTGAAGCAGAAGTCGATGATAATACGCGTCGTTTTATCAT",
+            record_2.seq
+        );
+        let finish = seqs.next();
+        assert!(finish.is_none());
+    }
+
+    #[test]
+    fn load_fa_gz_file_test() {
+        let reader = get_reader(PATH_FA_GZ).unwrap();
+        let mut seqs = Sequences::new(SeqFormat::Fasta, reader).unwrap();
+        let record_1 = seqs.next().unwrap();
+        assert_eq!("Record_1", record_1.id);
+        assert_eq!(
+            "GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACCAAGTTACCCTTAACAACTTAAGGGTTTTCAAATAGA",
+            record_1.seq
+        );
+        let record_2 = seqs.next().unwrap();
+        assert_eq!("Record_2", record_2.id);
+        assert_eq!(
+            "GTTCAGGGATACGACGTTTGTATTTTAAGAATCTGAAGCAGAAGTCGATGATAATACGCGTCGTTTTATCAT",
+            record_2.seq
+        );
+        let finish = seqs.next();
+        assert!(finish.is_none());
+    }
+
+    #[test]
+    fn parser_test() {
+        let input = ">Record_1\nACGTACGTACGT";
+        let reader = BufReader::new(input.as_bytes());
+        let mut seqs = Sequences::new(SeqFormat::Fasta, reader).unwrap();
+        let record_1 = seqs.next().unwrap();
+        assert_eq!("Record_1", record_1.id);
+        assert_eq!("ACGTACGTACGT", record_1.seq);
+        let finish = seqs.next();
+        assert!(finish.is_none());
+    }
+}

rsbio_seq-0.1.0/test_data/reads.fa

@@ -0,0 +1,5 @@
+>Record_1
+GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACCAAGTTACCCTTAACAACTTAAGGGTTTTCAAATAGA
+>Record_2
+GTTCAGGGATACGACGTTTGTATTTTAAGAATC
+TGAAGCAGAAGTCGATGATAATACGCGTCGTTTTATCAT

rsbio_seq-0.1.0/test_data/reads.fq

@@ -0,0 +1,8 @@
+@Read_1
+GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACCAAGTTACCCTTAACAACTTAAGGGTTTTCAAATAGA
++Read_1
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9ICIIIIIIIIIIIIIIIIIIIIDIIIIIII>IIIIII/
+@Read_2
+GTTCAGGGATACGACGTTTGTATTTTAAGAATCTGAAGCAGAAGTCGATGATAATACGCGTCGTTTTATCAT
++Read_2
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBIIIIIIIIIIIIIIIIIIIIIIIGII>IIIII-I)8I

rsbio_seq-0.1.0/tests/perf.py

@@ -0,0 +1,22 @@
+from tqdm import tqdm
+from Bio import SeqIO as BioSeqIO
+import sys
+from rsbio_seq import SeqIO as RsSeqIO
+
+
+if __name__ == "__main__":
+    assert len(sys.argv) == 3, "Must provide a valid sequence file and format"
+    for seq in tqdm(
+        RsSeqIO(sys.argv[1]),
+        desc="Rs-iteration",
+    ):
+        pass
+
+    for seq in tqdm(
+        BioSeqIO.parse(sys.argv[1], sys.argv[2]),
+        desc="Bio-iteration",
+    ):
+        pass
+
+# Rs-iteration:  28963522it [01:16, 379747.32it/s]
+# Bio-iteration: 28963522it [02:43, 177329.69it/s]

rsbio_seq-0.1.0/tests/test.py

@@ -0,0 +1,84 @@
+from rsbio_seq import SeqIO, Sequence
+import pathlib
+
+dir = pathlib.Path(__file__).parent
+
+
+def test_fa():
+    seqs = SeqIO(dir.joinpath("../test_data/reads.fa").as_posix())
+    seq: Sequence = next(seqs)
+    assert seq.id == "Record_1"
+    assert (
+        seq.seq
+        == "GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACCAAGTTACCCTTAACAACTTAAGGGTTTTCAAATAGA"
+    )
+    seq = next(seqs)
+    assert seq.id == "Record_2"
+    assert (
+        seq.seq
+        == "GTTCAGGGATACGACGTTTGTATTTTAAGAATCTGAAGCAGAAGTCGATGATAATACGCGTCGTTTTATCAT"
+    )
+
+
+def test_fa_gz():
+    seqs = SeqIO(dir.joinpath("../test_data/reads.fa.gz").as_posix())
+    seq: Sequence = next(seqs)
+    assert seq.id == "Record_1"
+    assert (
+        seq.seq
+        == "GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACCAAGTTACCCTTAACAACTTAAGGGTTTTCAAATAGA"
+    )
+    seq: Sequence = next(seqs)
+    assert seq.id == "Record_2"
+    assert (
+        seq.seq
+        == "GTTCAGGGATACGACGTTTGTATTTTAAGAATCTGAAGCAGAAGTCGATGATAATACGCGTCGTTTTATCAT"
+    )
+
+
+def test_fq():
+    seqs = SeqIO(dir.joinpath("../test_data/reads.fq").as_posix())
+    seq: Sequence = next(seqs)
+    assert seq.id == "Read_1"
+    assert (
+        seq.seq
+        == "GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACCAAGTTACCCTTAACAACTTAAGGGTTTTCAAATAGA"
+    )
+    assert (
+        seq.qual
+        == "IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9ICIIIIIIIIIIIIIIIIIIIIDIIIIIII>IIIIII/"
+    )
+    seq: Sequence = next(seqs)
+    assert seq.id == "Read_2"
+    assert (
+        seq.seq
+        == "GTTCAGGGATACGACGTTTGTATTTTAAGAATCTGAAGCAGAAGTCGATGATAATACGCGTCGTTTTATCAT"
+    )
+    assert (
+        seq.qual
+        == "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBIIIIIIIIIIIIIIIIIIIIIIIGII>IIIII-I)8I"
+    )
+
+
+def test_fq_gz():
+    seqs = SeqIO(dir.joinpath("../test_data/reads.fq.gz").as_posix())
+    seq: Sequence = next(seqs)
+    assert seq.id == "Read_1"
+    assert (
+        seq.seq
+        == "GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACCAAGTTACCCTTAACAACTTAAGGGTTTTCAAATAGA"
+    )
+    assert (
+        seq.qual
+        == "IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9ICIIIIIIIIIIIIIIIIIIIIDIIIIIII>IIIIII/"
+    )
+    seq: Sequence = next(seqs)
+    assert seq.id == "Read_2"
+    assert (
+        seq.seq
+        == "GTTCAGGGATACGACGTTTGTATTTTAAGAATCTGAAGCAGAAGTCGATGATAATACGCGTCGTTTTATCAT"
+    )
+    assert (
+        seq.qual
+        == "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBIIIIIIIIIIIIIIIIIIIIIIIGII>IIIII-I)8I"
+    )