rsbio-seq 0.1.5

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

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 --release # 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)

Reading from FASTA (fai/fai+gzi) index

Index reader supports fasta in raw text and bgzipped formats.

seqs = SeqReaderIndexed(
    "path/tp/seq.fa",
    "path/to/seq.fa.fai"
)
seq: Sequence = seqs["Record_1"]
print(seq.id)
print(seq.seq)
print(seq.desc)

"Record_2" in seqs # returns a boolean

For bgzipped fasta files, a gzi file is required.

seqs = SeqReaderIndexed(
    "path/tp/seq.fa.gz",
    "path/to/seq.fa.gz.fai",
    "path/to/seq.fa.gz.gzi",
)
seq: Sequence = seqs["Record_1"]
print(seq.id)
print(seq.seq)
print(seq.desc)

"Record_2" in seqs # returns a boolean

Using an invalid key will result in KeyError.

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.

Writing to FASTA with an Index (fai/fai+gzi)

Writing FASTA with an index can be performed in plain text and compressed forms. In compressed form the compression used is bgzip. In addition to fai there will also be a gzi file in compressed form. You can specify to compress using gz suffix at the end. Index paths are automatically inferred.

# Plain text
seq = Sequence("id", "desc", "ACGT") # id, description, sequence
writer = SeqWriter("out.fasta", True) # set index true
writer.write(seq)
writer.close()

# Compressed
seq = Sequence("id", "desc", "ACGT") # id, description, sequence
writer = SeqWriter("out.fa.gz", True) # set index true
writer.write(seq)
writer.close()

Planned soon for the major release v1.0.0

• Support for fastq Indexes

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!