Primavera

Primavera is a Python library to plan and analyze primer-based verification of DNA assemblies, using Sanger sequencing or verification PCR. It implements methods to design and select primers to ensure that the relevant assembly segments will be covered, and it

Usage

Primer selection

The following code assumes that a file available_primers.fa contains the labels and sequences of all available primers in the lab, and that the assemblies to be sequence-verified have annotations indicating the zones that the sequencing should cover and zones where primer annealing should be avoided.

https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Primavera/master/docs/_static/images/annotated_genbank.png

from primavera import PrimerSelector, Primer, load_record
import os

# LOAD ASSEMBLIES RECORDS AND AVAILABLE PRIMERS
records = [load_record(file_path, linear=False)
        for file_path in ['my_record_1.gb', 'my_record_2.gb'...]]
available_primers = Primer.list_from_fasta("example_primers.fa")

# SELECT THE BEST PRIMERS
selector = PrimerSelector(tm_range=(55, 70), size_range=(16, 25))
selected_primers = selector.select_primers(records, available_primers)

# PLOT THE COVERAGE AND WRITE THE PRIMERS IN A SPREADSHEET
selector.plot_coverage(records, selected_primers, 'coverage.pdf')
selector.write_primers_table(selected_primers, 'selected_primers.csv')

The returned selected_primers contains a list of lists of primers (one list for each construct). The PDF report returned looks like this:

https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Primavera/master/docs/_static/images/annotated_primer_selection.png

Sequencing Validation

(documentation for this feature is coming soon)

Installation

You can install Primavera through PIP

pip install primavera

To be able to generate plots and reports, run

pip install dna_features_viewer weasyprint

License = MIT

Primavera is an open-source software originally written at the Edinburgh Genome Foundry by Zulko and released on Github under the MIT licence (Copyright 2017 Edinburgh Genome Foundry, University of Edinburgh).

Everyone is welcome to contribute!

More biology software

https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Edinburgh-Genome-Foundry.github.io/master/static/imgs/logos/egf-codon-horizontal.png

Primavera is part of the EGF Codons synthetic biology software suite for DNA design, manufacturing and validation.

Examples

Primer selection example