Skip to content

Home

VARNA API is a Python interface for VARNA (v3-93), a Java lightweight component and applet for drawing the RNA secondary structure. VARNA allows users to produce drawing in a non-iteractive way via command line. However, the command line might be massive and complicate in some use cases. VARNA API aims to simplify such process. The online documentation is available.

Starting from v1.1.0, VARNA API uses 1-indexed to count RNA bases. The change aims to better align with ViennaRNA and the command line interface of VARNA.

VARNA api v2 is under the development with the help of JPype. We aim to provide a direct access to VARNA library while keeping backward compatibility.

Example

The command below highlights region 11-21 and adds a non-canonical base pair at position (14,20) on secondary structure ((((((.((((((........)))))).((((((.......))))))..)))))).

java -cp VARNAv3-93.jar fr.orsay.lri.varna.applications.VARNAcmd -structureDBN "((((((.((((((........)))))).((((((.......))))))..))))))" -o example.png -auxBPs "(14,20):color=#ff00ff" -highlightRegion "11-21"

The equivalence using VARNA API would be

from varnaapi import Structure
v = Structure(structure="((((((.((((((........)))))).((((((.......))))))..))))))")
v.add_highlight_region(11,21)
v.add_aux_BP(14, 20, edge5="s", color="#FF00FF")
v.savefig("example.png")

Installation

python3 -m pip install varnaapi

Basic Usage

Here, we show the basic usage of varnaapi. The first thing after importing varnaapi is to setup the location of VARNA if it's different than default.

import varnaapi
varnaapi.set_VARNA(path_to_VARNA)
Note

By default, the library assumes the VARNA v3-93 in the current folder is used (./VARNAv3-93.jar). To avoid setting the path each time, one can turn on the flag write via set_VARNA(path_to_VARNA, write=True) once. This stores the path into a configuration file and will be loaded automatically next time when varnaapi is used.

Each drawing in VARNA is an object of class inherited from BasicDraw. The standard class to draw from given secondary structure or/and RNA sequence is Structure.

ss = "((((((.((((((........)))))).((((((.......))))))..))))))"
v = varnaapi.Structure(structure=ss)

Print

One can call the member function BasicDraw.savefig() with given file name to save the drawing. The format is either png or svg, that VARNA will determine from the file name.

v.savefig("my_drawing.png")

While using jupyter notebook, one can use the member function BasicDraw.show() to display the drawing in the notebook

v.show()
Debug

Before v1.2, the corresponding command line to call VARNA is also printed. This is moved to logging.debug after v1.2. One can turn it on with

import logging
from varnaapi.settings import Logger
logging.basicConfig(level=logging.DEBUG)
Logger.setLevel(logging.DEBUG)

Style Configuration

In VARNA, one can chose the structure drawing algorithm, change the style for base pair, or hide backbone in drawing etc. The full list of parameters with default value can be found here. In library, the easiest way to modify these parameters is through the member function BasicDraw.update(). Some parameters, such as algorithm, can be set up via specific function. The rest will be supported in future update.

v.update(algorithm='naview', bpStyle='none', drawBackbone=False, bp='#006400')
Color parameters

Value for all color parameters in VARNA API should be readable by the object colour.Color, such as human color name, hex, RGB etc.

Save configuration

The library offers function to save the parameters setting in YAML format for the further use.

v.dump_param('config.yml')

Load configuration

There are two ways to load the saved configuration. The first one is using the member function of BasicDraw.

v.load_param('config.yml')
The second way is loading the configuration as a global setting in the opened session.
varnaapi.load_config('config.yml')

Parameter value priority order

VARNA API uses parameter values in the following order, i.e. if the value in the current order is undefined, then the next one is used

  • Value set by varnaapi.BasicDraw.update() or similar functions
  • Object Value loaded using varnaapi.BasicDraw.load_param()
  • Global values loaded using varnaapi.load_cofig()
  • Default parameter values.

Operations

In addition to changing drawing style, VARNA provides different operations on drawing, such as highlighting a region, adding auxiliary base pairs. This can be achieved by using the proper functions. We invite users to read API for more details.

v.add_highlight_region(1, 6, radius=20)
v.add_aux_bp(1, 10, color='red')

Hack mode

By default, VARNA api performs syntax check to verify the command line sent to VARNA is in the correct format. This might have conflict with non-standard VARNA versions, so that one might need to enable hack mode with varnaapi.enable_hack. See here for an example.

Questions and Bugs

Feel free to raise a github issue if you have a question or find a bug.

Credits

Please kindly cite VARNA supporting manuscript if you use VARNA API in your research. Download bibtex format.

Darty, K., Denise, A., & Ponty, Y. (2009). VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics, 25(15), 1974.