rsbio-seq 0.1.3

Description:

rsbioseq 0.1.3

RSBio-Seq






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RSBio-Seq intends to provide reading/writing facility on common sequence formats (FASTA/FASTQ) in both raw (fasta, fa, fna, fastq, fq) and compressed formats (.gz).
Installation
1. From PyPI (Recommended)
Use the following command to install from PyPI.
pip install rsbio-seq

2. Build and install from source
To build from source, make sure you have the following programs installed.

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

To build and install the development version of the wheel.
maturin develop # this installs the development version in the env
maturin develop --rust # this installs a release version in the env

To build a release mode wheel for installation, use this command.
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. The built wheel can be installed using this command.
pip install target/wheels/*.whl

Usage
Once installed you can import the library and use as follows.
Reading
from rsbio_seq import SeqReader, Sequence, ascii_to_phred

# each seq entry is of type Sequence
seq: Sequence

for seq in SeqReader("path/to/seq.fasta.gz"):
print(seq.id)
print(seq.seq)
# for fastq quality line
print(seq.qual) # prints IIII
print(ascii_to_phred(seq.qual)) # prints [40, 40, 40, 40]
# optional description attribute
print(seq.desc)

Writing
from rsbio_seq import SeqWriter, Sequence, phred_to_ascii

# 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", "IIII") # id, description, sequence, quality
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()

# writing gzipped with phred score translation
qual = phred_to_ascii([40, 40, 40, 40])
seq = Sequence("id", "desc", "ACGT", qual) # id, description, sequence, quality
writer = SeqWriter("out.fq.gz")
writer.write(seq)
writer.close()

Note: close() is only required if you want to read the file again in the same function/code scope. Closing opened files is a good practice either way.
We provide two utility functions for your convenience.

phred_to_ascii - convert phred scores list of numbers to a string
ascii_to_phred - convert the quality string to a list of numbers

RSBio-Seq reads and write quality string in ascii format only. Please use these helper functions to translate if you intend to read them.
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!