bseq

Python package for handling biological sequences and alignments

Quickstart

Install bseq

pip install bseq

Nucleotide sequence into FASTA format

from bseq.sequence import NuclSequence
seq = NuclSequence('test_seq_name', 'GATTACA', description='Test nucleotide sequence')
print(seq.fasta_format())

Import alignment from file

from bseq.reader import read_fasta_alignment
aln = read_fasta_alignment('/Users/Me/Downloads/seq.aln.fasta', 
                           seq_type='nucleotide', name='test_alignment', 
                           description='Test alignment for bseq')

Overview

bseq helps biologists import and manipulate biological sequences such as nucleotides, amino acids, and codons. Unlike other bioinformatics packages in Python, bseq solely focuses on analyzing and manipulating sequences and alignments.

Dependencies

bseq uses numpy for many alignment operations, and nose to test its source code. When using pip to install bseq, pip will automatically install numpy and nose.