Examples
--------

Note: all examples here are available in the ``examples/`` folder of the
code repository

.. contents::

Basic examples
--------------



Optimization with report
++++++++++++++++++++++++

.. literalinclude:: ../examples/optimization_with_report.py


Optimization of a circular sequence
+++++++++++++++++++++++++++++++++++

.. literalinclude:: ../examples/circular_sequence.py


Advanced examples
-----------------

Sequence standardization/domestication
++++++++++++++++++++++++++++++++++++++

.. literalinclude:: ../examples/scenarios/gene_domestication.py

Programmatic optimization of a full genome
++++++++++++++++++++++++++++++++++++++++++

.. literalinclude:: ../examples/scenarios/ecoli_genes_optimization.py


Creating a collection of compatible primers
+++++++++++++++++++++++++++++++++++++++++++

.. literalinclude:: ../examples/scenarios/primers_collection.py

Writing a custom Specification: 9-mer score
+++++++++++++++++++++++++++++++++++++++++++

.. literalinclude:: ../examples/scenarios/gen9_9mer_score_minimization.py


Creating a sequence without E. coli TF binding sites
++++++++++++++++++++++++++++++++++++++++++++++++++++

.. literalinclude:: ../examples/scenarios/sequence_without_tf_binding_sites.py

Constraints reports example
+++++++++++++++++++++++++++

.. literalinclude:: ../examples/reports/constraints_breaches_report/constraints_breaches_report.py