Allow download of sequences in several formats

[tberardini]

I'd like to be able to download the sequences in several formats.

Describe the solution you'd like

Desired formats:

1. FASTA with FASTA header that includes name, type of sequence and genomic coordinates
2. sequence blocks of 100 or so with genomic coordinates on one side

Describe alternatives you've considered

Copy paste will give raw sequence. Add FASTA header manually, break up into block with genomic coordinates added manually.

Additional context
This would be for any of the sequence view options.

[tberardini]

Including the genomic coordinates has the additional bonus of showing the user if the gene is on the forward or reverse strand.

[cmdcolin]

these are great suggestions...will see what we can do

[tberardini]

Checking on when this might rise to the top of the to-do list.

[cmdcolin]

thank you for the reminder, I am doing a bunch of work in some semi-related areas in the codebase and will see what I can do about getting this added!!

[tberardini]

Checking in again. :)

[cmdcolin]

@tberardini this is now merged to main, if you want to try it you can see it clicking a gene feature in our demo instance

https://jbrowse.org/code/jb2/main/?session=share-bXbhdpBOZL&password=T2jka

theres a lot of little details packed in but you can try it out to see. you can manually toggle on and off the "show coordinates" setting in the vertical "..." dropdown menu. it can show feature relative coordinates (e.g. starting from 0) for most feature types and the "Genomic w/ full introns" allows showing the genome-relative coordinates too.

thanks for pushing on this!

[tberardini]

@cmdcolin This is really cool and we've got 2.11.2 deployed in our sandbox now for testing. The download in FASTA format with the mixed casing is fantastic.

I'm having trouble finding the vertical "..." dropdown menu where one can specify display of the genomic coordinates.
Where should I see that?

our instance:

Unfortunately, when I click on your link, the features seem to be broken.

[cmdcolin]

you might have to clear your web browser cache and refresh the page. You can also get the main branch into your sandbox if you use "jbrowse upgrade --nightly" it's not fully released yet

[tberardini]

By not fully released, does that mean that if we updated to 2.11.2 recently, this wasn't included yet? I see the feature on your demo site but not yet on ours. It's definitely an improvement!

[tberardini]

The update just went to production. Here's what I see:

https://jbrowse2.arabidopsis.org/index.html?session=share-u7JIepHRMQ&password=XqWCl

[cmdcolin]

yes its not fully released yet, it's just on our "main branch" now which means itll likely get into the next release, and you can get the main branch builds using the "--nightly" flag (that just gets latest main branch)

if you wanna try out that nightly version and give any early feedback it could help us tailor it further before it gets to official release

[tberardini]

Ok, we will do that and I'll get back to you. When are you shooting for the next release?

[cmdcolin]

Probably early July or so

[tberardini]

Hi @cmdcolin We updated to the --nightly version and I see the new menu now!

What I haven't yet figured out is how to show the genomic coordinates like you had in your screenshot. For the 'show coordinates' the options see are shown above. Where is that setting?

[cmdcolin]

i actually removed the genomic coordinates because there was a bug with it. we can try to restore it though

[tberardini]

If possible, please restore the genomic coordinates for the options that include 'Genomic%'.

This is the feature that allows people to see clearly/download which strand of the chromosome encodes the gene (forward vs. reverse) and the position on the chromosome at the same time.

[cmdcolin]

@tberardini the genomic coordinates feature was added back by @carolinebridge if you want to try it out, can redownload the --nightly :)

[cmdcolin]

went ahead and released in v2.12.2

if you run into any issues, do let us know! might be able to close for now

[tberardini]

Sorry, am at a conference this week so I can’t test anything easily, I’ll let you know if I run into issues.

…

On Fri, Jun 21, 2024 at 9:03 AM Colin Diesh ***@***.***> wrote: went ahead and released in v2.12.2 if you run into any issues, do let us know! might be able to close for now — Reply to this email directly, view it on GitHub <#3873 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABGENV6BHKIYOEPR2EVKBPDZIQQCFAVCNFSM6AAAAAA363U7JWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOBSG4YTIOBQGQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[tberardini]

@cmdcolin This looks great. Clarification: what do the various colors mean?

no highlight = intron
green = CDS
blue = UTR
pink = ?

[cmdcolin]

great to hear! we should add some sort of legend...

• pink is the up/down stream sequence (in the settings menu you can configure how many base pairs of up/downstream sequence to fetch)
• blue is UTR
• green/yellow is CDS
• no highlight is intron

[cmdcolin]

note also that "green" is used to highlight of non-gene feature types

[tberardini]

yes, a legend would be great. Thanks for the clarification.