scottcain

[[0,0,230218,0,"NCBI:BK006935.2","chrI","chrI","chrI","SGD","chromosome",
  {"Sublist":
     [[1,0,801,-1,"SGD:S000028862","SGD:S000028862",
       "Telomeric region on the left arm of Chromosome I", "TEL01L","TEL01L","Telomeric region on the left arm of Chromosome I; composed of an X element core sequence, X element combinatorial repeats, and a short terminal stretch of telomeric repeats","chrI","SGD",
       [{"end":"801","name":"TEL01L_X_element","seq_id":"chrI","source":"SGD","start":"337","strand":"-","type":"X_element"},
        {"end":"336","name":"TEL01L_X_element_combinatorial_repeat","seq_id":"chrI","source":"SGD","start":"63","strand":"-","type":"X_element_combinatorial_repeat"},
        {"end":"62","name":"TEL01L_telomeric_repeat_1","seq_id":"chrI","source":"SGD","start":"1","strand":"-","type":"telomeric_repeat"},
        {"end":"801","id":"TEL01L_telomere","name":"TEL01L_telomere","seq_id":"chrI","source":"SGD","start":"1","strand":"-","type":"telomere"}],

scottcain

###
Y34D9B.1b       WormBase        polypeptide     1       529     .       .       .       ID=Y34D9B.1b;uniprot_id=Q9N532;wormbase_geneid=WBGene00003238;wormbase_genename=mig-1;wormbase_protein=CE24204
Y34D9B.1b       WormBase        CDS     1       529     .       .       .       ID=Y34D9B.1b_exon_boundaries;uniprot_id=Q9N532;wormbase_geneid=WBGene00003238;wormbase_genename=mig-1;wormbase_protein=CE24204
Y34D9B.1b       WormBase        exon    1       43      .       .       .       Parent=Y34D9B.1b_exon_boundaries
Y34D9B.1b       WormBase        exon    43      90      .       .       .       Parent=Y34D9B.1b_exon_boundaries
Y34D9B.1b       WormBase        exon    91      161     .       .       .       Parent=Y34D9B.1b_exon_boundaries
Y34D9B.1b       WormBase        exon    162     208     .       .       .       Parent=Y34D9B.1b_exon_boundaries
Y34D9B.1b       WormBase        exon    209     239     .       .       .       Parent=Y34D9B.1b_exon_boundaries
Y34D9B.1b       WormBase        exon    239     2

scottcain

(base) MacBook-Pro-6:tmp cain$  git clone https://github.com/scottcain/seqpanel.git
Cloning into 'seqpanel'...
remote: Enumerating objects: 709, done.
remote: Counting objects: 100% (106/106), done.
remote: Compressing objects: 100% (52/52), done.
remote: Total 709 (delta 59), reused 70 (delta 52), pack-reused 603
Receiving objects: 100% (709/709), 2.09 MiB | 3.73 MiB/s, done.
Resolving deltas: 100% (402/402), done.
(base) MacBook-Pro-6:tmp cain$ cd seqpanel/lib
(base) MacBook-Pro-6:lib cain$ yarn

scottcain

Delivered-To: cain.cshl@gmail.com
Received: by 2002:a17:906:b28f:b0:997:d052:1521 with SMTP id q15csp2320014ejz;
        Thu, 20 Jul 2023 11:23:56 -0700 (PDT)
X-Received: by 2002:a17:906:2086:b0:992:387:44d1 with SMTP id 6-20020a170906208600b00992038744d1mr10559686ejq.7.1689877436292;
        Thu, 20 Jul 2023 11:23:56 -0700 (PDT)
ARC-Seal: i=1; a=rsa-sha256; t=1689877436; cv=none;
        d=google.com; s=arc-20160816;
        b=IT7V4jo8D9BrWIAVXBS9We0z+BGfnrPNwjBoqiZUQe0KUxTjkN7if6q5bQaedXFv8t
         rxFU3CAfCURBDoqPBHIhMyuYYqWNWN2q1kAIStYCfpQ1tE0mu7bIFI8jzhKF9ca+/FcH
         vMDes1pKfi7sPAR9ZoRJq9XkcrmC+KP5pVK1Th2gmrjnoe2fGseoCtyu3+BNlYz36cKX

scottcain

    {
      "type": "SyntenyTrack",
      "trackId": "c_elegans.c_brenneri.paf-1669841807246",
      "name": "c_elegans.c_brenneri.paf",
      "assemblyNames": [
        "c_elegans_PRJNA13758",
        "c_brenneri_PRJNA20035"
      ],
      "adapter": {
        "type": "PAFAdapter",

scottcain

<script src="https://unpkg.com/react@16/umd/react.development.js" crossorigin></script><script src="https://unpkg.com/react-dom@16/umd/react-dom.development.js" crossorigin></script><script src="https://unpkg.com/@jbrowse/react-linear-genome-view/dist/react-linear-genome-view.umd.development.js" crossorigin></script>

<p>We're using the JBrowse Linear Genome View!</p>

<div id="jbrowse2_linear_genome_view" width="500px">this is where the browser should be</div>

  <script>
    function create_jbrowse2() {
      const { createElement } = React
      const { render } = ReactDOM

scottcain

//this exact JS works just fine at http://scottca.in/node/3
// but at https://staging.wormbase.org/species/c_elegans/gene/WBGene00001340#09f6--10
// the exact same JS (with an extra fetch to get the releaseVersion) nearly entirely
// works but does NOT offset the track labels--that is the only difference.
//
// Weird

<script src="https://unpkg.com/react@16/umd/react.development.js" crossorigin></script><script src="https://unpkg.com/react-dom@16/umd/react-dom.development.js" crossorigin></script><script src="https://unpkg.com/@jbrowse/react-linear-genome-view/dist/react-linear-genome-view.umd.development.js" crossorigin></script>

function create_jbrowse2() {

scottcain

{
  "exports" : {
    "c_elegans_PRJNA13758_assembly" : "./c_elegans_PRJNA13758_assembly.js" 
  }
}

scottcain

.... lots of stuff that looks ok ...
^[[32mwebpack_1      |^[[0m verbose 574.985439042 Removing extraneous file "/home/node/client/node_modules/write/node_modules/.bin".
^[[32mwebpack_1      |^[[0m [4/4] Building fresh packages...
^[[32mwebpack_1      |^[[0m verbose 577.406487021 ^[[35m^[[1mLove JSS? You can now support us on open collective:^[[22m^[[39m
^[[32mwebpack_1      |^[[0m  > ^[[34mhttps://opencollective.com/jss/donate^[[0m
^[[32mwebpack_1      |^[[0m verbose 578.906366582 Thank you for using core-js ( https://github.com/zloirock/core-js ) for polyfilling JavaScript standard library!
^[[32mwebpack_1      |^[[0m
^[[32mwebpack_1      |^[[0m The project needs your help! Please consider supporting of core-js on Open Collective or Patreon:
^[[32mwebpack_1      |^[[0m > https://opencollective.com/core-js
^[[32mwebpack_1      |^[[0m > https://www.patreon.com/zloirock

scottcain

{
    "label" : "SpCas9 NGG PAM sites",
    "unsafeMouseover" : true,
    "unsafePopup" : true,
    "type":"CanvasFeatures",
    "category" : "CRISPR_Cas9 sgRNA predictions",
    "key" : "SpCas9 NGG PAM sites",
    "style" : {
       "color" : "RebeccaPurple",
       "height" : 5