Metadata-Version: 1.0
Name: dnachisel
Version: 0.1.3
Summary: Optimize DNA sequences under constraints.
Home-page: UNKNOWN
Author: Zulko
Author-email: UNKNOWN
License: MIT
Description: DNA Chisel
        ==========
        
        DNA Chisel is a Python library to optimize the nucleotides of DNA sequences with respect to a set of constraints and optimization objectives. It can be used for codon-optimizing the genes of a sequence for a particular organism, modifying a sequence to meet the constraints of a DNA provider while preserving genes, and much more.
        
        
        DNA Chisel comes with more than 15 types of optimizations and constraints and allows users to define new specifications in Python, making the library suitable for a large range of automated sequence design applications, or complex custom design projects.
        
        Example of use
        ---------------
        
        .. code:: python
        
            from dnachisel import *
        
            # DEFINE THE OPTIMIZATION PROBLEM
        
            random_sequence = random_dna_sequence(10000)
            problem = DnaOptimizationProblem(
                sequence=random_sequence,
                constraints=[AvoidPattern(enzyme_="BsaI"),
                             EnforceGCContent(mini=0.3, maxi=0.7, window=50)],
                objectives=[CodonOptimize(species='e_coli', location=(500, 1300))]
            )
        
            # SOLVE THE CONSTRAINTS, OPTIMIZE WITH RESPECT TO THE OBJECTIVE
        
            problem.resolve_constraints()
            problem.optimize()
        
            # PRINT SUMMARIES TO CHECK THAT CONSTRAINTS PASS
        
            print(problem.constraints_text_summary())
            print(problem.objectives_text_summary())
        
        Infos
        -----
        
        **PIP installation:**
        
        .. code:: bash
        
          pip install dnachisel
        
        **Web documentation:**
        
        `<https://edinburgh-genome-foundry.github.io/DnaChisel/>`_
        
        **Github Page**
        
        `<https://github.com/Edinburgh-Genome-Foundry/DnaChisel>`_
        
        **Live demo**
        
        `<http://cuba.genomefoundry.org/sculpt_a_sequence>`_
        
        **License:** MIT, Copyright Edinburgh Genome Foundry
        
        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/
        
        DNA Chisel is part of the `EGF Codons <https://edinburgh-genome-foundry.github.io/>`_ synthetic biology software suite for DNA design, manufacturing and validation.
        
Keywords: DNA optimization constraints synthetic biology
Platform: UNKNOWN
