Riboswitch cartoon

In [1]:

import varnaapi

import varnaapi

In [2]:

aptamer = '(((((...((((((((.....)))))...)))...)))))............................'
length = len(aptamer)
color = 'lightgreen'

aptamer = '(((((...((((((((.....)))))...)))...)))))............................' length = len(aptamer) color = 'lightgreen'

In [3]:

v = varnaapi.Structure(structure=aptamer)
v.update(bpStyle='none', baseNum='white', drawBackbone=False, drawBases=False, fillBases=False, spaceBetweenBases=0.5)
v.add_highlight_region(1, length, radius=5, fill=color, outline=color)
v.savefig('ribo_cartoon.png', show=True)

v = varnaapi.Structure(structure=aptamer) v.update(bpStyle='none', baseNum='white', drawBackbone=False, drawBases=False, fillBases=False, spaceBetweenBases=0.5) v.add_highlight_region(1, length, radius=5, fill=color, outline=color) v.savefig('ribo_cartoon.png', show=True)

['java', '-cp', 'VARNA-module.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', '', '-structureDBN', '(((((...((((((((.....)))))...)))...)))))............................', '-o', 'ribo_cartoon.png', '-spaceBetweenBases', '0.5', '-bpStyle', 'none', '-drawBases', 'False', '-baseNum', '#ffffff', '-drawBackbone', 'False', '-fillBases', 'False', '-highlightRegion', '1-68:radius=5.0,fill=#90ee90,outline=#90ee90']

Output file: ribo_cartoon.png

One can store the configuration for further

In [4]:

v.dump_param('cartoon.yml')

v.dump_param('cartoon.yml')

In [5]:

aptSeq = 'NNNNGAUACCAGCAUCGUCUUGAUGCCCUUGGCAGCNNNNNNNNNNNNNNNNNNNNNNNNUUUUUUUU'
regions = [(1,4), (37,60)]

aptSeq = 'NNNNGAUACCAGCAUCGUCUUGAUGCCCUUGGCAGCNNNNNNNNNNNNNNNNNNNNNNNNUUUUUUUU' regions = [(1,4), (37,60)]

In [6]:

v = varnaapi.Structure(sequence=aptSeq.replace('N', ' '), structure=aptamer)
v.load_param('cartoon.yml')
for i, j in regions:
    v.add_highlight_region(i, j, radius=5, fill=color, outline=color)
v.savefig('ribo_cartoon.png', show=True)

v = varnaapi.Structure(sequence=aptSeq.replace('N', ' '), structure=aptamer) v.load_param('cartoon.yml') for i, j in regions: v.add_highlight_region(i, j, radius=5, fill=color, outline=color) v.savefig('ribo_cartoon.png', show=True)

['java', '-cp', 'VARNA-module.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', '    GAUACCAGCAUCGUCUUGAUGCCCUUGGCAGC                        UUUUUUUU', '-structureDBN', '(((((...((((((((.....)))))...)))...)))))............................', '-o', 'ribo_cartoon.png', '-spaceBetweenBases', '0.5', '-bpStyle', 'none', '-drawBases', 'False', '-baseNum', '#ffffff', '-drawBackbone', 'False', '-fillBases', 'False', '-highlightRegion', '1-4:radius=5.0,fill=#90ee90,outline=#90ee90;37-60:radius=5.0,fill=#90ee90,outline=#90ee90']

Output file: ribo_cartoon.png

One can set the configuration as global

In [7]:

varnaapi.load_config('cartoon.yml')

varnaapi.load_config('cartoon.yml')

In [8]:

specRegions = [(5,36)]
darker = 'green'

specRegions = [(5,36)] darker = 'green'

In [9]:

v = varnaapi.Structure(sequence=' '*60+'UUUUUUUU', structure=aptamer)
for i, j in regions:
    v.add_highlight_region(i, j, radius=5, fill=color, outline=color)
for i, j in specRegions:
    v.add_highlight_region(i, j, radius=5, fill=darker, outline=darker)
v.savefig('ribo_cartoon.png', show=True)

v = varnaapi.Structure(sequence=' '*60+'UUUUUUUU', structure=aptamer) for i, j in regions: v.add_highlight_region(i, j, radius=5, fill=color, outline=color) for i, j in specRegions: v.add_highlight_region(i, j, radius=5, fill=darker, outline=darker) v.savefig('ribo_cartoon.png', show=True)

['java', '-cp', 'VARNA-module.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', '                                                            UUUUUUUU', '-structureDBN', '(((((...((((((((.....)))))...)))...)))))............................', '-o', 'ribo_cartoon.png', '-spaceBetweenBases', '0.5', '-bpStyle', 'none', '-drawBases', 'False', '-baseNum', '#ffffff', '-drawBackbone', 'False', '-fillBases', 'False', '-highlightRegion', '1-4:radius=5.0,fill=#90ee90,outline=#90ee90;37-60:radius=5.0,fill=#90ee90,outline=#90ee90;5-36:radius=5.0,fill=#008000,outline=#008000']

Output file: ribo_cartoon.png