biostrings 0.0.2

Efficient manipulation of genomic sequences

biostrings

Efficient manipulation of genomic sequences in Python, inspired by the design of Bioconductor's Biostrings package.

The core design relies on a "pool and ranges" memory model:

• DNAStringSet stores all sequences in a single contiguous block of memory (the pool).
• Individual sequences are defined by start and width coordinates (the ranges).
• Slicing a DNAStringSet returns a view (a new set of ranges pointing to the same pool), making subsetting operations virtually instantaneous and memory-free, regardless of the data size.

Install

To get started, install the package from PyPI

pip install biostrings

Quick Start

Working with Single Sequences

The DNAString class represents a single DNA sequence. It enforces the IUPAC DNA alphabet and supports efficient byte-level operations.

from biostrings import DNAString

# Create a DNA string
dna = DnaString("TTGAAAA-CTC-N")
print(dna)
# Output: TTGAAAA-CTC-N

# Basic operations
print(len(dna))            # 13
print(dna[0:3])            # DnaString(length=3, sequence='TTG')

# Reverse Complement
# Handles IUPAC ambiguity codes correctly (e.g., N -> N, M -> K)
rc = dna.reverse_complement()
print(rc)
# Output: N-GAG-TTTTCAA

Working with Sets of Sequences

The DNAStringSet is the primary container for handling collections of sequences (e.g., reads from a FASTA file).

from biostrings import DNAStringSet

# Efficiently create a set from a list of strings
seqs = [
    "ACGT",
    "GATTACA",
    "TTGAAAA-CTC-N",
    "ACGTACGT"
]
dss = DNAStringSet(seqs, names=["s1", "s2", "s3", "s4"])

print(dss)
# Output:
# <DNAStringSet of length 4>
#   [ 1]   4 ACGT                 s1
#   [ 2]   7 GATTACA              s2
#   [ 3]  13 TTGAAAA-CTC-N        s3
#   [ 4]   8 ACGTACGT             s4

Note

This project has been set up using BiocSetup and PyScaffold.