rsbio-seq 0.1.2

RSBio-Seq is a fast and light-weight sequence reading library (built on top of rust bio crate).

RSBio-Seq

RSBio-Seq intends to provide just reading facility on common sequence formats (FASTA/FASTQ) in both raw and compressed formats.

Installation

1. From PyPI (Recommended)

Simple use the following command

pip install rsbio-seq

2. Build and install from source

To build you need to have the following installed.

• Rust - https://www.rust-lang.org/tools/install
• Maturin - https://www.maturin.rs/installation
• Python environment with Python >=3.9

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 for installation

maturin build --release

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.

Usage

Once installed you can import the library and use as follows.

Reading

from rsbio_seq import SeqReader, SeqWriter, Sequence

# reading
for seq in SeqReader("path/to/seq.fasta.gz"):
    print(seq.id)
    print(seq.seq)
    # for fastq quality line
    print(seq.qual)
    # optional description attribute
    print(seq.desc)

Writing

# writing fasta
seq = Sequence("id", "desc", "ACGT") # id, description, sequence
writer = SeqWriter("out.fasta")
writer.write(seq)
writer.close()

# writing fastq
seq = Sequence("id", "desc", "ACGT") # id, description, sequence
writer = SeqWriter("out.fastq")
writer.write(seq)
writer.close()

# writing gzipped
seq = Sequence("id", "desc", "ACGT", "IIII") # id, description, sequence, quality
writer = SeqWriter("out.fq.gz")
writer.write(seq)
writer.close()

Note: close() is needed if you want to read within the same program scope. Otherwise, rust will automatically do this for you.

Authors

• Anuradha Wickramarachchi https://anuradhawick.com
• Vijini Mallawaarachchi https://vijinimallawaarachchi.com

Support and contributions

Please get in touch via author websites or GitHub issues. Thanks!