Comments (5)
+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.
from dnafeaturesviewer.
Thanks. The script will be released freely soon :-)
from dnafeaturesviewer.
Using pysam.VariantFile
I am am able to convert variation to a collection of Bio.SeqFeature
which are translated (BiopythonTranslator
) to a collection of dna_features_viewer.GraphicRecord.GraphicRecord
The result is quite good, I stuck currently to display a coord label for each tick of those features on the ruler. Did you know how to do this ?
from dnafeaturesviewer.
Hi, thanks for the question & answer, that looks great! I personally didn't know, so if you don't mind sending the script, then we can include it here and as one of the Examples. To answer the original question, if you can produce the variants as Biopython records, then you can use Geneblocks or CUBA compare-two-sequences.
from dnafeaturesviewer.
No I didn't look at it closely, but I see now that this is Covid-19! Nice.
from dnafeaturesviewer.
Related Issues (20)
- BiopythonTranslator: SeqFeatures with location_operator='join' get wrong position
- Labels overlap whan sharing axis HOT 2
- Feature request: x_lim best-fit HOT 6
- Enhanced Bokeh support for multiple plots HOT 2
- Linking exon annotations with intron lines, and other things. HOT 5
- Add an example which plots sequence features not starting from 0 HOT 5
- truncated scaffolds from gff files HOT 4
- figure is not coming
- type hints support HOT 1
- Error on BioPython v1.8.0 HOT 9
- type error for global variable related to BioPython update HOT 2
- sequences display from 1 not 0 ? HOT 1
- How to solve the memory problem of batch plotting? HOT 3
- Overlapping arrows in circular DNA HOT 1
- CircularGraphicRecord does not work. Unable to make circular graphs HOT 1
- UndefinedSequenceError with gff files and BioPython 1.81
- Oval or diamond/octagon in addition to arrows for displayed features? HOT 1
- 'Seq' object has no attribute 'defined' HOT 2
- feature location in a join, how to correnctly translate HOT 3
- Dna first project
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from dnafeaturesviewer.