Open mictadlo opened 2 years ago
this doesn't necessarily help with your apollo and jbrowse 1, but jbrowse 2 has code that can calculate the protein sequence client side. example screenshot (can get live demo at https://jbrowse.org/jb2 also)
I am not able to see the code on BitBucket you linked (looks like I don't have permission), but I might have an idea. You can access the sequence by using Apollo's Web Service APIs. Here is an example of how this would look using a feature on our demo sequence:
curl --header 'Content-Type:application/json' --data '{"organismString":"Honeybee","sequenceName":"Group1.25","featureName":"afaad855-7b99-4e86-8828-b3b7cfb5891d","type":"peptide","username":"demo@demo.com","password":"demo"}' http://demo.genomearchitect.io/Apollo2/sequence/sequenceByName
or equivalently in JS
fetch('http://demo.genomearchitect.io/Apollo2/sequence/sequenceByName', {
method: 'POST',
headers: { 'Content-Type': 'application/json' },
body: JSON.stringify({
organismString: 'Honeybee',
sequenceName: 'Group1.25',
featureName: 'afaad855-7b99-4e86-8828-b3b7cfb5891d',
type: 'peptide',
username: 'demo@demo.com',
password: 'demo',
}),
})
.then(response => response.text())
.then(console.log)
The possible type
s are genomic, cds, cdna, and peptide. Let me know if this doesn't work for you.
Hi all, Apollo allows to drag-n-drop a gene into the yellow field, and from the gene menu, you can select Get Sequence and get, for example, the peptide sequence for the gene as shown below:
The above solution works, but most users forget to delete the genes from the yellow Apollo's annotation field. Therefore, I wrote a small web app based on Python's Flask framework, which can be found here. To add it to Apollo, I need to add the following lines to trackList.json for the gene track:
The user needs to select a gene and click right-mouse click and select Get Sequence from the menu:
However, the problem with my solution is that I need to create a new database for each annotation. How is it possible to access Apollo's database, or how can Get Sequence be extracted from Apollo and replace my code?
I really appreciate any help you can provide. Michal