synbiopython.genbabel.simplednaplot

Synbiopython (c) Global BioFoundry Alliance 2020

Synbiopython is licensed under the MIT License.

This module is to implement the simple plotting of the gene circuit using the modified code from quickplot.py in DNAplotlib library # added quickplot style for writing Regulations. # added new Regulation type: Derepression

Reference:

https://github.com/VoigtLab/dnaplotlib

Install:

pip install dnaplotlib

class synbiopython.genbabel.simplednaplot.SimpleDNAplot.SimpleDNAplot[source]

Bases: object

Class to generate SBOL visual compliant gene circuit diagram. Regulation type: Connection, Activation, Repression, Derepression Each of the part will be numbered sequentially based on the part type/module from left to right starting from index 0. Example: p0-r0-c0-t0-p1-r1-c1-t1 for two modules with promoter, RBS, coding region, and terminator. Input = “p.pTet r.rbs34 c.orange.LacI t p.pLac r.rbs32 c.green.TetR t” Regulations = “c0->p1.Repression c1->p0.Repression” # The default color is black if color is not specified

static compute_dnalength(part, part_length)[source]

Calculate the position for the to_part or from_part for plotting arrows automatically.

Parameters

  • part (str) – the to_part or from_part

  • part_length (list of str) – all the parts with sequential numbering starting from 0

Returns

dna length

Return type

float

plot_circuit(Input, Regulation=None, savefig=None)[source]

Plot the SBOL-compliant gene circuit figure.

Parameters

  • Input (str) – Input design from users

  • Regulation (str) – Regulation strings from users

  • savefig (str, optional) – path to store the output figure

Returns

max dna design length and export the gene circuit figure

Return type

float

set_circuit_design(Input, Regulation=None)[source]

Generate the dictionary list containing circuit design information.

Parameters

  • Input (str) – a string containing the individual type of part, followed by color and name separated by a space.

  • Regulation (str, optional) – a string containing the from_part to the to_part connected by an arrow. Type of interaction is specified after the topart followed by the color. Default color of black is used is not specified.

Returns

The part information and Regulations stored in the form of list of dictionaries.

Return type

list of dict