Primer selection example

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.

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:

Infos

PIP installation:

pip install primavera

Web documentation: https://edinburgh-genome-foundry.github.io/Primavera/

Github page: https://github.com/Edinburgh-Genome-Foundry/Primavera

Live demo: http://cuba.genomefoundry.org/select_primers

License: MIT

Copyright 2017 Edinburgh Genome Foundry, University of Edinburgh

More biology software

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