Caravagene reference manual
graph LR;
param1(category) --> Part
param2(label) --> Part
param3(name) --> Construct
param4(note) --> Construct
param5(name) --> ConstructList
param6(note) --> ConstructList
Part --> Construct
Part --> Construct
Part --> Construct
Construct --> ConstructList
Construct --> ConstructList
Construct --> ConstructList
style param1 fill:none,stroke:none;
style param2 fill:none,stroke:none;
style param3 fill:none,stroke:none;
style param4 fill:none,stroke:none;
style param5 fill:none,stroke:none;
style param6 fill:none,stroke:none;
- class caravagene.Part(category, label='', sublabel='', subscript='', reversed=False, bg_color='none')[source]
Represent a genetic part.
- Parameters:
category – Either ‘promoter’, ‘CDS’… Defines the symbol displayed for this part.
label – String that will be displayed on top of the part.
sublabel – Note that will be written in grey below the label.
subscript – Note that will be written below the part.
reversed – True/False. Whether the part is in direct or indirect sense.
bg_color – String representing any html color, which will be used as background to highlight this part.
- static from_dict(part_dict)[source]
Create a part from a dictionary.
This is intended for Schema imports from JSON in web applications. This dictionary should have the same parameters as the __init__ function (other parameters will be ignored).
- property style
Define the CSS style from the part’s parameters.
- class caravagene.Construct(parts, name='', note='')[source]
Represent a genetic construct with several parts.
- Parameters:
parts – A list of Parts, in the order in which they appear in the construct. Alternatively, a pandas dataframe can be provided, with columns ‘label’, ‘category’, ‘sublabel’, ‘subscript’, ‘style’. The last column, ‘style’ can be for instance “bg:green bold”.
name – Name of the construct. Will be displayed on top of the construct’s plot.
note – Some text that will be displayed between the construct’s name and plot.
- class caravagene.ConstructList(constructs, title='auto', note='', size=13, font='Helvetica', orientation='portrait', width=600, page_size='A4', use_google_fonts=False)[source]
Represent a genetic construct will several parts.
- Parameters:
constructs – A list of Constructss, in the order in which they appear in the plot. Alternatively, a path to an excel spreadsheet can be provided (see docs for explanations on the spreadsheet format).
title – Title for this list of constructs. Will be displayed on top of the plots.
note – Some text that will be displayed between the title and the plots.
size – Size of the font for labels, which also scales the size of sublabel, subscript, and the symbol itself.
font – Name of the font to use for all texts.
orientation – ‘portrait’ or ‘landscape’. Orientation of the page when exporting to PDF.
width – Page width when exporting to an image.
page_size – Page format when exporting to PDF.
use_google_fonts – Whether the font should be obtained from Google Fonts (will only work with an Internet access).
- static from_dict(csts_dict)[source]
Create a constructs list from a dictionary.
This is intended for Schema imports from JSON in web applications. This dictionary should have the same parameters as the __init__ function (other parameters will be ignored).