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alternative .csv file types for feature annotation #862

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GretaHultqvist opened this issue Oct 10, 2022 · 26 comments
Open

alternative .csv file types for feature annotation #862

GretaHultqvist opened this issue Oct 10, 2022 · 26 comments

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@GretaHultqvist
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GretaHultqvist commented Oct 10, 2022 •
edited by tnrich
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@tnrich
I am switshing to use OVE from prevoiusly using Benchling where I had several hundreds of proteins annotated. In benchling you can save features both as proteins and as DNA. Is this possible for OVE? I have my features saved as protiens in 95% of the cases since to me the DNA sequence is not so important but the resulting protein is. If not is this something that you could implement? In benchling you can export all the features that you have annotated and it would be great if this file could be used to auto annotate the proteins in OVE but the files seems in compatible.

The CSV file I export from benchlign looks like below. For me it would be extremely valuable if this file could be read by OVE.

Name,Feature,Type,Color,Match type
15 long linker based on the one I designed,APGSGTGGGSGSAPG,,#85DAE9,protein
20 aa linker based on the one I designed,APGGSGGGTGGGSGGGSAPG,,#C7B0E3,protein
22 aa linker,GPGSGGGGSGGGGSGGGGSGPG,,#f58a5e,protein
38 aa lkong linker,APGGSGGGSGGGSGGGSGGGSGGGTGGGSGGGSAGSPG,,#75C6A9,protein
3d6 variable domain LC,YVVMTQTPLTLSVTIGQPASISCKSSQSLLDSDGKTYLNWLLQRPGQSPKRLIYLVSKLDSGVPDRFTGSGSGTDFTLKISRIEAEDLGLYYCWQGTHFPRTFGGGTKLEIK,,#ff9ccd,protein
3d6 variable HC,EVKLVESGGGLVKPGASLKLSCAASGFTFSNYGMSWVRQNSDKRLEWVASIRSGGGRTYYSDNVKGRFTISRENAKNTLYLQMSSLKSEDTALYYCVRYDHYSGSSDYWGQGTTVTVS,,#f58a5e,protein
@tnrich
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tnrich commented Oct 11, 2022

Hi @GretaHultqvist thanks for making a ticket here!

I just want to make sure I understand what you're asking. Are you talking about wanting to be able to complete the following dialog:
image
Using the csv file that is directly exported from benchling and contains mostly protein annotations?

Thanks!
Thomas

@GretaHultqvist
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GretaHultqvist commented Oct 11, 2022 via email •
edited by tnrich
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@tnrich
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tnrich commented Oct 11, 2022

Hi @GretaHultqvist thanks for your response,

I'll see what I can do, this isn't the highest priority for me right now but it also shouldn't be too tough to allow protein annotations to be included in the uploaded CSV for the auto-annotation tool. Fully matching the benchling CSV would be a significant amount of additional work.

Another question I have.. when these annotations get auto-annotated onto the sequence you have open, what should those annotations look like:

  1. Should those annotations be features be of type CDS?
  2. Should those features be "saved as proteins" in some other way? I'm unfamiliar with how the protein annotations work in benchling so some guidance would be needed here.

@GretaHultqvist
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GretaHultqvist commented Oct 12, 2022 via email

@tnrich
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tnrich commented Oct 12, 2022

@GretaHultqvist could you re-attach the image to your message above? I don't think it made it here.

I think you'll need to do so thru github.com and not via email. Thanks again for your explanation!

@GretaHultqvist
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GretaHultqvist commented Oct 12, 2022 via email

@tnrich
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tnrich commented Oct 12, 2022

@GretaHultqvist please try uploading it from #862, not via email response.

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tnrich commented Oct 12, 2022

This is what I'm seeing on my end:
image

@GretaHultqvist
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Screenshot 2022-10-12 at 08 59 42

[](url)

@GretaHultqvist
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GretaHultqvist commented Oct 12, 2022 via email

@tnrich
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tnrich commented Nov 2, 2022

Hey @GretaHultqvist,

Please note I have NOT yet added the underlying functionality necessary to support auto annotating PROTEIN sequences. However I have been working on adding an upload CSV wizard to our underlying component system. Here's the issues tracking that

TeselaGen/teselagen-react-components#293
TeselaGen/teselagen-react-components#289

Here's what the v1 experience will look like for you as a user of OVE adding your custom CSV file:

image

After dragging in your CSV file you'll see this:
image

Selecting Feature for the sequence field:
image

After hitting the Review and Edit Data button:
image

After hitting Add File:
image

Let me know if this workflow makes sense to you. Once I have time to add the underlying protein auto-annotate functionality I'll let you know and enable it in conjunction with this feature.

Cheers!
Thomas

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tnrich commented Nov 18, 2022

@GretaHultqvist are you using the desktop application of OVE?

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GretaHultqvist commented Nov 20, 2022 via email

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tnrich commented Nov 29, 2022

@GretaHultqvist would you mind trying out the new release here and see if my changes solve this issue for you? https://github.com/TeselaGen/ove-electron/releases/tag/v1.5.3

Cheers!

@GretaHultqvist
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GretaHultqvist commented Nov 29, 2022 via email

@GretaHultqvist
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Screenshot 2022-12-01 at 14 23 18
So I get this error message when trying to install. Could it be due to the M2 processor?

@tnrich
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tnrich commented Dec 1, 2022

Hmm shouldn't be seeing that. What happens if you right click the downloaded file and ask to open it? Maybe something is wrong with the latest release however.. I'll look into it today. Thanks!

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tnrich commented Dec 1, 2022

@GretaHultqvist hmm looks like something changed between releases.. I'll need to look into it further but I am seeing the same thing on my m1 mac. I'll un-publish that release now since it appears to be corrupted.

@GretaHultqvist
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GretaHultqvist commented Dec 1, 2022 via email

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tnrich commented Dec 1, 2022

Hey @GretaHultqvist could you try out https://github.com/TeselaGen/ove-electron/releases/tag/v1.5.4 and see if it works for you? You'll ned to right click the app the first time you try to run it.

@GretaHultqvist
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GretaHultqvist commented Dec 1, 2022 via email

@GretaHultqvist
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GretaHultqvist commented Dec 1, 2022 via email

@tnrich
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tnrich commented Dec 1, 2022

@GretaHultqvist whoops looks like the auto annotate enhancement that adds protein matching to OVE didn't make it into the release I just published. Not sure why that didn't happen but I must not have updated the dep. Let me update everything and republish. At that point you should see a new column here:
image

I'll let you know when the new release comes out

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tnrich commented Dec 1, 2022

Ok, this should be the updated version here @GretaHultqvist
https://github.com/TeselaGen/ove-electron/releases/tag/v1.5.5

@GretaHultqvist
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I have tested version 1.5.5 now and still not sure how to get the protein feature or annotation.
Screenshot 2022-12-02 at 10 22 18

When I for instance choose new feature in the screen shot above I get these options
Screenshot 2022-12-02 at 10 24 14
Which does not have an option to select save as protein. Is is somewhere else I should be looking?
Greta

@tnrich
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tnrich commented Dec 2, 2022

@GretaHultqvist it seems like there is some other feature you're expecting to see that you haven't yet described.. All I added was a way to auto-annotate new features using a CSV with a match type of "protein". I also made it so if you used a file with slightly different formatting, the import system would try its best to match up the headers and allow you to edit the data if needed.

Here is the standard auto-annotate flow:

  1. File > Auto Annotate > Auto Annotate Features

  2. image

  3. Upload a file with the matchType column set to 'protein':

image

  1. That should allow features to be auto-annotated on the sequence via an Amino Acid string

Note you can also use the CSV file you pasted in your first comment, the one you were asking to be able to be imported into OVE:

The CSV file I export from benchling looks like below. For me it would be extremely valuable if this file could be read by OVE.

Name,Feature,Type,Color,Match type
15 long linker based on the one I designed,APGSGTGGGSGSAPG,,#85DAE9,protein
20 aa linker based on the one I designed,APGGSGGGTGGGSGGGSAPG,,#C7B0E3,protein
22 aa linker,GPGSGGGGSGGGGSGGGGSGPG,,#f58a5e,protein
38 aa lkong linker,APGGSGGGSGGGSGGGSGGGSGGGTGGGSGGGSAGSPG,,#75C6A9,protein
3d6 variable domain LC,YVVMTQTPLTLSVTIGQPASISCKSSQSLLDSDGKTYLNWLLQRPGQSPKRLIYLVSKLDSGVPDRFTGSGSGTDFTLKISRIEAEDLGLYYCWQGTHFPRTFGGGTKLEIK,,#ff9ccd,protein
3d6 variable HC,EVKLVESGGGLVKPGASLKLSCAASGFTFSNYGMSWVRQNSDKRLEWVASIRSGGGRTYYSDNVKGRFTISRENAKNTLYLQMSSLKSEDTALYYCVRYDHYSGSSDYWGQGTTVTVS,,#f58a5e,protein

Please let me know if you still have any questions with the new protein auto annotation flow

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