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What Python Libraries Exist For Drawing Genes/Features/Intervals?

I am working on new software for exploring genetic variation and genome annotations. One feature I would like to add is the ability to plot features (gene's, SNPs, SVs, etc.) in a given genomic region. What libraries are you aware of for producing "plots" or images like this in Python. Essentially, I am looking for something similar to Perl's Bio::Graphics module.

So far, I've seen that GenomeTools has a Python interface, but I am looking for possible alternatives.

visualization python api
• 16,696 views • link
updated by Biostar Biostar • written by Aaronquinlan Aaronquinlan

4 answers

Have a look at BioGraphy by Andrea Pierleoni. It is probably going to be integrated into BioPython soon.

Example of BioGraphy output (from the tutorial):

alt text

Another alternative is GenomeDiagram. I can not reach the page linked in the article now, but this library should be included in the newer versions of BioPython. You can see some examples in the BioPython cookbook, chapter 15.

Example of GenomeDiagram output:

alt text

• 355 views • link
written by Giovanni M Dall'Olio Giovanni M Dall'Olio

These look promising, thanks.

• 0 views • link
written by Aaronquinlan Aaronquinlan

I have tryed to use BioGraphy and got it via: 

git clone git://github.com/apierleoni/BioGraPy

After the two steps python setup.py build and python setup.py install, I tested the tutorial code from http://apierleoni.github.io/BioGraPy/tutorial.html:

from biograpy import Panel, tracks, features
panel=Panel(fig_width=900, padding = 25)#initialize a drawer, and add some padding
test_track = tracks.BaseTrack(features.Simple(name = 'feat1', start = 100, end = 356, ),
                              features.Simple(name = 'feat2', start = 30, end = 856, ),
                              features.Simple(name = 'feat3', start = 400, end = 700, ),
                              sort_by = 'None',)
panel.add_track(test_track)
panel.save('basic_test.png')

However, after this I got the following error message by using the ipython notebook (python 2.7):

AttributeError                            Traceback (most recent call last)
<ipython-input-1-050f14eab25c> in <module>()
      4                               features.Simple(name = 'feat2', start = 30, end = 856, ),
      5                               features.Simple(name = 'feat3', start = 400, end = 700, ),
----> 6                               sort_by = 'None',)
      7 panel.add_track(test_track)
      8 panel.save('basic_test.png')

/home/linux/anaconda2/lib/python2.7/site-packages/biograpy-1.0b0dev_r0-py2.7.egg/biograpy/tracks.pyc in __init__(self, *args, **kwargs)
    151         self.norm = kwargs.get('norm', None)# normalizing function, if None build one. could be any function taking a value an returning a float between 0 and 1
    152         if not self.norm:
--> 153             self.norm = colors.normalize(vmin = self.min_score, vmax = self.max_score)
    154 
    155 

AttributeError: 'module' object has no attribute 'normalize'

Does somebody know how to solve this problem?

Thanks

• 1 views • link
updated by Ram Ram • written by jochenfra • jochenfra

BioPython can now do diagrams as well. The picture below is for restriction analysis, but you get the idea.

alt text

• 2 views • link
written by Michael Schubert Michael Schubert

I haven't tried these, but also check out:

  1. willow by Titus brown--I think that's tied to pygr somehow
  2. GenomeViewer which uses Wx for rendering.
• 1 views • link
written by brentp brentp

Also, there is http://genes.mit.edu/burgelab/miso/docs/sashimi.html

• 0 views • link
updated by Ram Ram • written by bw. bw.

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