Metadata-Version: 2.4
Name: primavera
Version: 0.1.14
Summary: Primer selection + data analysis for DNA assembly validation.
Author: Zulko
License-Expression: MIT
Project-URL: Homepage, https://github.com/Edinburgh-Genome-Foundry/Primavera
Keywords: DNA,assembly,sequencing,primer,design
Description-Content-Type: text/x-rst
License-File: LICENCE.txt
Requires-Dist: numpy
Requires-Dist: Biopython
Requires-Dist: proglog
Requires-Dist: flametree
Requires-Dist: pandas
Requires-Dist: dna_features_viewer
Requires-Dist: dnachisel
Dynamic: license-file

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 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.

.. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Primavera/master/docs/_static/images/annotated_genbank.png
   :width: 600px

.. code:: python

    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:

.. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Primavera/master/docs/_static/images/annotated_primer_selection.png
   :width: 600px


Infos
-----

**PIP installation:**

.. code:: bash

    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
---------------------

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

Primavera is part of the `EGF Codons <https://edinburgh-genome-foundry.github.io/>`_ synthetic biology software suite for DNA design, manufacturing and validation.
