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vanya-antonov / django_gtdb2

GeneTackDB-2 based on Biopython and powered by Django
GNU General Public License v3.0
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Visualize the relative location of chlIDH and cobNST genes #4

Open gottalottarock opened 4 years ago

gottalottarock commented 4 years ago

Visualize the relative location of chlIDH and cobNST genes as diagram on a genetic locus. See some advices here (e.g. Biopython Genome Diagram):

https://www.biostars.org/p/337928/ https://www.biostars.org/p/338136/ https://biopython-cn.readthedocs.io/zh_CN/latest/en/chr17.html

vanya-antonov commented 4 years ago

https://www.biostars.org/p/304382/

vanya-antonov commented 4 years ago

https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer

vanya-antonov commented 4 years ago

About different file formtats: https://genome.ucsc.edu/FAQ/FAQformat.html

vanya-antonov commented 4 years ago

Zero-vs-one based indexing: https://www.biostars.org/p/84686/

https://genome.ucsc.edu/FAQ/FAQtracks#tracks1 Our internal database representations of coordinates always have a zero-based start and a one-based end. We add 1 to the start before displaying coordinates in the Genome Browser. Therefore, they appear as one-based start, one-based end in the graphical display. The refGene.txt file is a database file, and consequently is based on the internal representation.

We use this particular internal representation because it simplifies coordinate arithmetic, i.e. it eliminates the need to add or subtract 1 at every step. If you use a database dump file but would prefer to see the one-based start coordinates, you will always need to add 1 to each start coordinate.

If you submit data to the browser in position format (chr#:##-##), the browser assumes this information is 1-based. If you submit data in any other format (BED (chr# ## ##) or otherwise), the browser will assume it is 0-based. You can see this both in our liftOver utility and in our search bar, by entering the same numbers in position or BED format and observing the results. Similarly, any data returned by the browser in position format is 1-based, while data returned in BED format is 0-based.

vanya-antonov commented 4 years ago

Sample code for dna_features_viewer lib https://drive.google.com/drive/folders/1cr36eR3-EPUnXBP6frjYAlICECk9qvSK?usp=sharing