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How to display differences from Variant Calling File?

See original GitHub issue


I would like to use your awesome library with pysam in order to display the difference between two sequences. I see they are GeneBlock for this purpose. So how to create a such instance from a list of variations ?


best regards

Issue Analytics

  • State:closed
  • Created 3 years ago
  • Comments:5 (3 by maintainers)

github_iconTop GitHub Comments

bioinfornaticscommented, Jan 26, 2021

Thanks. The script will be released freely soon 😃

Zulkocommented, Jan 26, 2021

+1 for @veghp 's answer above, please share the script if you can! Btw @veghp did you guess what famous sequence this is?

display a coord label for each tick of those features on the ruler. Did you know how to do this ?

One way is to use Matplotlib’s ax.set_xticks([list of indices]), but this may create collisions if your indices are too close from one another. Another way is to add the index to the feature label, for instance "535\nReplaced G->T". This way Dna Features Viewer should detect close labels and display them under one another. Cosmetic pro tip: you can use ax2.invert_yaxis() on the bottom ax so that the Replaced G->T annotations will appear below the ax rather than above.

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