2.5D module drawing with hack mode

This notebook presents the usage of VARNA API hack mode to draw RNA 2.5D module with non-standard VARNA version (commit a463cfe).

In [1]:

import varnaapi

import varnaapi

In [2]:

dbn = "..((......)).."
v = varnaapi.Structure(structure=dbn)
v.show()

dbn = "..((......)).." v = varnaapi.Structure(structure=dbn) v.show()

['java', '-cp', './VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', '', '-structureDBN', '..((......))..', '-o', '/tmp/tmpw3x76tym.png']

Output file: /tmp/tmpw3x76tym.png

Assume that the hairpin loop (4,11) above is a 2.D module containing a non-canonical basepair (5,9) with type cSH. Let's try to draw it using add_aux_BP function.

In [3]:

v = varnaapi.Structure(structure=dbn)
v.add_aux_BP(5,9, edge5="s", edge3="h", color='green')
v.show()

v = varnaapi.Structure(structure=dbn) v.add_aux_BP(5,9, edge5="s", edge3="h", color='green') v.show()

['java', '-cp', './VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', '', '-structureDBN', '..((......))..', '-o', '/tmp/tmp8ilw7aoz.png', '-auxBPs', '(5,9):edge5=s,edge3=h,color=#008000']

Output file: /tmp/tmp8ilw7aoz.png

As we can see, the drawing is different than we would expect, the non-canonical basepair breaks the hairpin loop into two loops. This is because the standard VARNA (v3.93) will try to complete the secondary structure by adding as many non-crossing basepairs as possible from the auxiliary list. The non-standard VARNA version from commit a463cfe allows us to keep bases in the original positions while adding the auxiliary basepairs with option keep. However, the keep option cannot pass the syntax check in normal mode.

In [4]:

v = varnaapi.Structure(structure=dbn)
v.add_aux_BP(5,9, edge5="s", edge3="h", color='green', keep=True)
v.show()

v = varnaapi.Structure(structure=dbn) v.add_aux_BP(5,9, edge5="s", edge3="h", color='green', keep=True) v.show()

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[4], line 2
      1 v = varnaapi.Structure(structure=dbn)
----> 2 v.add_aux_BP(5,9, edge5="s", edge3="h", color='green', keep=True)
      3 v.show()

File ~/miniconda3/envs/varnaapi/lib/python3.9/site-packages/varnaapi/models.py:113, in BasicDraw.add_aux_BP(self, i, j, edge5, edge3, stericity, color, thickness, **kwargs)
    100 """Add an additional base pair `(i,j)`, possibly defining and using custom style
    101 
    102 Args:
   (...)
    109     thickness: Base-pair thickness
    110 """
    111 assert_valid_interval(self.length, i, j)
--> 113 self.aux_BPs.append((i, j, _BPStyle(edge5=edge5, edge3=edge3, stericity=stericity, color=color, thickness=thickness, **kwargs)))

File ~/miniconda3/envs/varnaapi/lib/python3.9/site-packages/varnaapi/param.py:360, in _BPStyle.__init__(self, **kwargs)
    358             raise TypeError('Value of {} should be one of {}'.format(key, BP_CHOICES[key]))
    359     else:
--> 360         raise TypeError('{} is not a valid keyword'.format(key))
    361 self.values = res

TypeError: keep is not a valid keyword

In order to use the non-standard version, VARNA API requires to turn on the hack mode, which will turn off most of the checks and allow us to pass additional options

In [5]:

varnaapi.enable_hack()

varnaapi.enable_hack()

Then, we set the path to the hacked version and draw the structure again

In [6]:

varnaapi.set_VARNA('VARNA-module.jar')
v = varnaapi.Structure(structure=dbn)
v.add_aux_BP(5,9, edge5="s", edge3="h", color='green', keep=True)
v.show()

varnaapi.set_VARNA('VARNA-module.jar') v = varnaapi.Structure(structure=dbn) v.add_aux_BP(5,9, edge5="s", edge3="h", color='green', keep=True) v.show()

['java', '-cp', 'VARNA-module.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', '', '-structureDBN', '..((......))..', '-o', '/tmp/tmp6gvy016s.png', '-auxBPs', '(5,9):edge5=s,edge3=h,color=#008000,keep=True']

Output file: /tmp/tmp6gvy016s.png

We can also set the command line option -keepAuxBPs to True if we want to keep all basepairs in auxiliary list as non-canonical.

In [7]:

v = varnaapi.Structure(structure=dbn)
v.add_aux_BP(5, 9, edge5="s", edge3="h", color='green')
v.add_aux_BP(6, 8, edge5="wc", edge3="h", color='red')
v.update(keepAuxBPs=True)
v.show()

v = varnaapi.Structure(structure=dbn) v.add_aux_BP(5, 9, edge5="s", edge3="h", color='green') v.add_aux_BP(6, 8, edge5="wc", edge3="h", color='red') v.update(keepAuxBPs=True) v.show()

['java', '-cp', 'VARNA-module.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', '', '-structureDBN', '..((......))..', '-o', '/tmp/tmpd1u867zl.png', '-keepAuxBPs', 'True', '-auxBPs', '(5,9):edge5=s,edge3=h,color=#008000;(6,8):edge3=h,color=#ff0000']

Output file: /tmp/tmpd1u867zl.png