Skip to main content

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 2017 Edinburgh Genome Foundry, University of Edinburgh

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


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

primavera-0.1.14.tar.gz (26.6 kB view details)

Uploaded Source

Built Distribution

primavera-0.1.14-py3-none-any.whl (28.9 kB view details)

Uploaded Python 3

File details

Details for the file primavera-0.1.14.tar.gz.

File metadata

  • Download URL: primavera-0.1.14.tar.gz
  • Upload date:
  • Size: 26.6 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/6.1.0 CPython/3.12.9

File hashes

Hashes for primavera-0.1.14.tar.gz
Algorithm Hash digest
SHA256 ac3be9144a4e61206f154e597811f3a4ef831e7c19809137168df1bab9163984
MD5 9277e435f3380051e45d4346342ccaeb
BLAKE2b-256 6d84b608f520a8f36e2a9d808e842e159bbddb1b9d66266508019fb6b2511a46

See more details on using hashes here.

Provenance

The following attestation bundles were made for primavera-0.1.14.tar.gz:

Publisher: publish.yml on Edinburgh-Genome-Foundry/Primavera

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

File details

Details for the file primavera-0.1.14-py3-none-any.whl.

File metadata

  • Download URL: primavera-0.1.14-py3-none-any.whl
  • Upload date:
  • Size: 28.9 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/6.1.0 CPython/3.12.9

File hashes

Hashes for primavera-0.1.14-py3-none-any.whl
Algorithm Hash digest
SHA256 92e5c60091bb735ab459f03a121de13ca7d5da47f0a416a30f5f66205c8b90f6
MD5 41250bca236ccea37d33b339bcf09b01
BLAKE2b-256 bdcf840304bf277d253629d793b7d40f3c34aac54485e60f9d6ce166da319704

See more details on using hashes here.

Provenance

The following attestation bundles were made for primavera-0.1.14-py3-none-any.whl:

Publisher: publish.yml on Edinburgh-Genome-Foundry/Primavera

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Fastly CDN Google Download Analytics Pingdom Monitoring Sentry Error logging StatusPage Status page