barcodeEZ

barcodeEZ is a Python package for designing complex, combinatorial DNA barcode libraries for molecular cloning.

The package allows design and creation of a site-aware Barcodes object. It is built around sites, expandable positions, restriction-enzyme boundaries, optimized overhangs, and optional fixed sequences. barcodeEZ draws orthogonal barcode sequence from a prebuilt corpus, assembles forward and reverse oligos, screens them for unwanted sequence content, and exports a ready-to-order oligo pool.

What it does

• Design a library structure from restriction-enzyme boundaries — use the built-in default panel or supply your own enzymes.
• Add positions within each site for combinatorial, multi-position barcoding (up to 8 positions per site), with automatically assigned optimized internal overhangs.
• Generate barcodes of any length from a corpus of ~30,000 orthogonal 60-mers shipped with the package.
• Attach fixed sequences to either end of a site.
• Validate against restriction sites and undesired motifs, automatically swapping out any contaminated barcode.
• Inspect the whole design as a pandas DataFrame.
• Export a single-stranded oligo order form as CSV.

Installation

pip install barcodeEZ

The barcode corpus ships with the package; biopython and pandas are installed automatically.

A minimal example

from barcodeEZ import Barcodes

b = Barcodes(n_sites=2)             # two barcoded sites, default enzymes
b.generate_barcodes(bc_len=20, n_barcodes=96)
b.validate()                        # screen + replace contaminated barcodes
b.write_order_form('library.csv')   # export the oligo pool

API

All functionality is accessed through the Barcodes(n_sites, custom_enzymes=None) object. Methods return self and can be chained.

Method	Purpose
add_positions(*, n_per_site)	Add combinatorial positions per site (call before generating)
generate_barcodes(bc_len, n_barcodes)	Draw barcodes and assemble oligos
add_fixed_sequence(seq, site, side)	Attach a fixed flanking sequence to a site
validate(ignore_defaults=False, motifs=None)	Screen and replace barcodes containing unwanted motifs
view()	Return the full library as a pandas DataFrame
write_order_form(file, metadata=False)	Export the oligo pool as CSV; metadata=True adds site, position, and barcode columns
print_structure()	Print the site/enzyme layout

See the full documentation for parameter details and examples.

Requirements

• Python ≥ 3.10
• biopython ≥ 1.81, pandas (installed automatically with pip)