benjamin-lee/dnavisualization.org

🧬📈 Turn DNA sequences into interactive visualizations

dnavisualization.org's Issues

First send hash to server to see if already transformed before uploading seq

Wrap the example load button in a b-col

The element inside of a b-row needs to be a b-col. So this:

<b-row>
      <b-dropdown
        split
        split-href="#foo/bar"
        text="Load Example"
        class="m-2"
        @click="transformExampleSequences"
      >
        <b-dropdown-item href="#">Sars-Cov2</b-dropdown-item>
        <b-dropdown-item href="#">HDV</b-dropdown-item>
        <b-dropdown-item href="#">HCV</b-dropdown-item>
      </b-dropdown>
      <b-col class="pl-0">
        <b-form-file
          v-model="uploadedFile"
          class="w-50"
          placeholder="Choose a file or drop it here..."
          drop-placeholder="Drop file here..."
          accept=".fasta, .fa, .fna, .fas, .frn, .ffn, .txt"
        ></b-form-file>
      </b-col>
    </b-row>

should be

<b-row>
<b-col cols=2>
      <b-dropdown
        split
        split-href="#foo/bar"
        text="Load Example"
        class="m-2"
        @click="transformExampleSequences"
      >
        <b-dropdown-item href="#">Sars-Cov2</b-dropdown-item>
        <b-dropdown-item href="#">HDV</b-dropdown-item>
        <b-dropdown-item href="#">HCV</b-dropdown-item>
      </b-dropdown>
</b-col>
      <b-col class="pl-0">
        <b-form-file
          v-model="uploadedFile"
          class="w-50"
          placeholder="Choose a file or drop it here..."
          drop-placeholder="Drop file here..."
          accept=".fasta, .fa, .fna, .fas, .frn, .ffn, .txt"
        ></b-form-file>
      </b-col>
    </b-row>

The cols=2 tell us that we only want the button to be two columns wide.

Uncaught TypeError: window.parse_fasta is not a function

Loading a fasta file doesn't work on the latest code from the main branch. I see these errors in Chrome developers view:

home.js:111 Uncaught TypeError: window.parse_fasta is not a function
    at Object.load (home.js:111)
    at FileReader.reader.(:5000/anonymous function) (http://127.0.0.1:5000/static/js/filereader.js:347:31)

Support for multiple visualization methods

• Add button to control visualization method (default to Squiggle)
• Send method to back end along with seq
• Store transformed sequences as xxxxxxx.METHOD.parquet.sz
• When querying, send the viz method
• Cache the different viz methods in the seqs variable (wontfix)
• Update the axes

Fix WASM switch cases to support lowercase

Load sample data button

We can use HBB as our demo for now, since that seems to be the standard demo of DNA sequence visualization

Switch vue-plotly libraries

Unless David-Desmaisons/vue-plotly#26 can be fixed, we'll need to switch back to https://github.com/statnett/vue-plotly since it doesn't produce gigantic bundles.

Graph div is not aligned properly

Integrate TelselaGen Parser

Add tooltips to describe methods on hover

Unable to paste sequences multiple times

Should be able to paste a sequence and then paste another sequence.

Allow sequence pasting from the toolbar

Fix the favicon

When adding sequences later, change the default zoom to include them

Move the clear button into the remove sequences modal

It doesn't make a ton of sense to have a separate button

Use v-b-tooltip.hover directive rather than component

It seems that using the tooltip component is breaking the b-button-toolbar component. The directive will probably work better: https://bootstrap-vue.org/docs/components/tooltip#tooltips

Support multiple download methods and sizes

I've already done it for one, just need to have a button that triggers a modal for choosing your data format and dimensions

Report an issue button

Link to GH issues with a bug report template

Pasting FASTA with non supported bases does not yield error message

Describe the bug
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To Reproduce
Steps to reproduce the behavior:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior
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Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. iOS]
• Browser [e.g. chrome, safari]
• Version [e.g. 22]

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Support downsampling large sequences

Custom "export" button

Right now, we're using the default highcharts export button, but it's possible use a custom button to trigger exporting to maintain our visual style.

https://api.highcharts.com/class-reference/Highcharts.Chart%23exportChart#exportChart

Deactivate automerging of updates

At least until there is testing of the plotting. This update might break things: AssemblyScript/assemblyscript#1559

Add support for y axis zooming for Gates

Enable changing the graph title

Use a modal with a form input wired up to a button

Randic labels are off

With

>example
ATGC

you get

Make example button load HDV

Integrate WASM into transformation pipeline

Track the file for an uploaded sequence

Color code graph by file or by sequence

This is the same as file mode vs sequence mode.

Disable the submit button on the Jumbotron if there is no pasted sequence

Add support for uploading multiple files at the same time

Make file uploading work

Add support for downloading example data

Enable switching between visualization methods after submission

Steps:

1. Create a currentMethod attribute in the Vuex state.
2. Create a button that mutates the state.
3. In the visualization, use the current method's visualization and dispatch the transformation action if it doesn't exist yet.

configure load example split button

add Sars-CoV2, etc.

Switch from pad-top to pt-2

"Loading" spinner while transforming files

So the page doesn't seem to freeze while computing

Deduplicate file uploads

Let's say a user uploads a file and then uploads it again, don't plot it twice if:

1. It has the same filename
2. The hash of the file is the same

Right now, it plots it twice as two identical lines:

Reject non fasta files and alert user

Allow the deletion of sequences and files that have been submitted

Fix jumbotron buttons on small screen

Allow upload of multiple files from toolbar

Rescale y axis when setting an x range

Hide Jumbotron if there are sequences visualized

Make y zooming work

Don't allow submission of sequences with non-ATGC methods

When method != squiggle

Clear uploaded filename from filepicker after upload

I uploaded BoNT.fasta and you can see it's still there in the box

When querying, also limit by y coordinate for better speed

Tooltips have broken html

It shows like this: Bases plotted along a unit vector. Captures GC skew. <var>x</var>-coordinates do not map to base position. No support for non-ATGC bases.

for these, just remove the var tags

Automatically set axis labels to match visualization method

This depends on #80.