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Primer selection + data analysis for DNA assembly validation

Project description

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 can generate simple (but approximative) plots summarizing the results of a batch of Sanger sequencing.

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.

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

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 Edinburgh Genome Foundry

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.

Project details


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Filename, size & hash SHA256 hash help File type Python version Upload date
primavera-0.1.5.tar.gz (26.2 kB) Copy SHA256 hash SHA256 Source None Feb 17, 2018

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