DEV: performance tweaks and docs

Cargo.toml

@@ -1,12 +1,12 @@
 [package]
 name = "rsbio-seq"
-version = "0.1.1"
+version = "0.1.2"
 edition = "2021"
 authors = [
     "Anuradha Wickramarachchi <anuradhawick@gmail.com>",
     "Vijini Mallawaarachchi <viji.mallawaarachchi@gmail.com>",
 ]
-description = "RSBio-Seq is a python wrapper for rust bio crate to provide fast sequence reading."
+description = "RSBio-Seq is a fast and light-weight sequence reading library (built on top of rust bio crate)."
 readme = "README.md"
 license-file = "LICENSE"
 

README.md

@@ -5,9 +5,19 @@
 [![PyPI - Version](https://img.shields.io/pypi/v/rsbio-seq)](https://pypi.org/project/rsbio-seq/)
 [![Upload to PyPI](https://github.com/anuradhawick/rsbio-seq/actions/workflows/pypi.yml/badge.svg)](https://github.com/anuradhawick/rsbio-seq/actions/workflows/pypi.yml)
 
-RSBio intends to provide just reading facility on common sequence formats (FASTA/FASTQ) in both raw and compressed formats.
+RSBio-Seq intends to provide just reading facility on common sequence formats (FASTA/FASTQ) in both raw and compressed formats.
 
-## Build and install from source
+## Installation 
+
+### 1. From PyPI (Recommended)
+
+Simple use the following command
+
+```bash
+pip install rsbio-seq
+```
+
+### 2. Build and install from source
 
 To build you need to have the following installed.
 
@@ -20,26 +30,21 @@ maturin develop # this installs the development version in the env
 maturin develop --rust # this installs a release version in the env
 ```
 
-To build a wheel
+To build a wheel for installation
 
 ```bash
 maturin build --release
 ```
 
-You will find the `whl` file inside the `target/wheels` directory.
-
-## Install from PyPI
+You will find the `whl` file inside the `target/wheels` directory. Your `whl` file will have a name depicting your python environment and CPU architecture.
 
-Simple use the following command
-
-```bash
-pip install rsbio-seq
-```
 
 ## Usage
 
 Once installed you can import the library and use as follows.
 
+### Reading
+
 ```python
 from rsbio_seq import SeqReader, SeqWriter, Sequence
 
@@ -51,7 +56,11 @@ for seq in SeqReader("path/to/seq.fasta.gz"):
     print(seq.qual)
     # optional description attribute
     print(seq.desc)
+```
 
+### Writing
+
+```python
 # writing fasta
 seq = Sequence("id", "desc", "ACGT") # id, description, sequence
 writer = SeqWriter("out.fasta")

pyproject.toml

@@ -11,6 +11,12 @@ classifiers = [
     "Programming Language :: Python :: Implementation :: PyPy",
 ]
 dynamic = ["version", "readme", "description", "license", "authors"]
+keywords = ["bioinformatics", "genomics"]
+
+[project.urls]
+Documentation = "https://github.com/anuradhawick/rsbio-seq/"
+"Bug Tracker" = "https://github.com/anuradhawick/rsbio-seq/issues"
+"Source Code" = "https://github.com/anuradhawick/rsbio-seq/"
 
 [tool.maturin]
 features = ["pyo3/extension-module"]

src/writer.rs

@@ -2,6 +2,7 @@ use crate::seq::{SeqFormat, Sequence};
 use flate2::{write::GzEncoder, Compression};
 use std::{fs::File, io::Write};
 
+#[inline]
 fn wrap_string_no_whitespace(s: &str, width: usize) -> String {
     let mut result = String::with_capacity(s.len() + s.len() / width);
     let mut i = 0;
@@ -47,11 +48,13 @@ impl Writer {
         }
     }
 
+    #[inline]
     pub fn write(&mut self, seq: Sequence, wrap: Option<u32>) -> Result<(), String> {
         let writer = match &mut self.writer {
             WriterType::Gzip(gz) => gz as &mut dyn Write,
             WriterType::Plain(file) => file as &mut dyn Write,
         };
+
         match self.format {
             SeqFormat::Fasta => {
                 let seq_str = if let Some(wrap) = wrap {
@@ -62,38 +65,33 @@ impl Writer {
                 } else {
                     seq.seq
                 };
-                writer.write_all(b">").map_err(|e| e.to_string())?;
-                writer
-                    .write_all(seq.id.as_bytes())
-                    .map_err(|e| e.to_string())?;
-                writer.write_all(b" ").map_err(|e| e.to_string())?;
-                writer
-                    .write_all(seq.desc.as_bytes())
-                    .map_err(|e| e.to_string())?;
-                writer.write_all(b"\n").map_err(|e| e.to_string())?;
-                writer
-                    .write_all(seq_str.as_bytes())
-                    .map_err(|e| e.to_string())?;
-                writer.write_all(b"\n").map_err(|e| e.to_string())?;
+                let mut buffer =
+                    Vec::with_capacity(4 + seq.id.len() + seq.desc.len() + seq_str.len());
+
+                buffer.extend_from_slice(b">");
+                buffer.extend_from_slice(seq.id.as_bytes());
+                buffer.extend_from_slice(b" ");
+                buffer.extend_from_slice(seq.desc.as_bytes());
+                buffer.extend_from_slice(b"\n");
+                buffer.extend_from_slice(seq_str.as_bytes());
+                buffer.extend_from_slice(b"\n");
+                writer.write_all(&buffer).map_err(|e| e.to_string())?;
             }
             SeqFormat::Fastq => {
-                writer.write_all(b"@").map_err(|e| e.to_string())?;
-                writer
-                    .write_all(seq.id.as_bytes())
-                    .map_err(|e| e.to_string())?;
-                writer.write_all(b" ").map_err(|e| e.to_string())?;
-                writer
-                    .write_all(seq.desc.as_bytes())
-                    .map_err(|e| e.to_string())?;
-                writer.write_all(b"\n").map_err(|e| e.to_string())?;
-                writer
-                    .write_all(seq.seq.as_bytes())
-                    .map_err(|e| e.to_string())?;
-                writer.write_all(b"\n+\n").map_err(|e| e.to_string())?;
-                writer
-                    .write_all(seq.qual.as_bytes())
-                    .map_err(|e| e.to_string())?;
-                writer.write_all(b"\n").map_err(|e| e.to_string())?;
+                let mut buffer = Vec::with_capacity(
+                    7 + seq.id.len() + seq.desc.len() + seq.seq.len() + seq.qual.len(),
+                );
+
+                buffer.extend_from_slice(b"@");
+                buffer.extend_from_slice(seq.id.as_bytes());
+                buffer.extend_from_slice(b" ");
+                buffer.extend_from_slice(seq.desc.as_bytes());
+                buffer.extend_from_slice(b"\n");
+                buffer.extend_from_slice(seq.seq.as_bytes());
+                buffer.extend_from_slice(b"\n+\n");
+                buffer.extend_from_slice(seq.qual.as_bytes());
+                buffer.extend_from_slice(b"\n");
+                writer.write_all(&buffer).map_err(|e| e.to_string())?;
             }
         }
         Ok(())