Scott Cain scottcain
scottcain
/ Problems webpacking wormbase_jbrowse
Created
June 17, 2022 18:24
Problems webpacking wormbase/jbrowse
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| .... 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
/ JBrowse CRISPR regex tracks
Created
July 1, 2021 20:03
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| { | |
| "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 |
scottcain
/ gist:e3e4aa6e7f390490772600a7aa82508d
Created
July 1, 2021 18:33
non-functional jbrowse regex track
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| { | |
| "label" : "SpCas9 NGG PAM sites", | |
| "unsafeMouseover" : true, | |
| "unsafePopup" : true, | |
| "type":"CanvasFeatures", | |
| "category" : "1testing", | |
| "key" : "SpCas9 NGG PAM sites", | |
| "metadata" : { | |
| "shortInfo" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif." | |
| }, |
scottcain
/ gist:e37065016751f0818b5c8c3267024931
Created
May 18, 2021 20:24
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| Step 8/29 : WORKDIR /usr/share/nginx/html/tools/protein_schematic | |
| ---> Running in 44c21469489b | |
| Removing intermediate container 44c21469489b | |
| ---> 3e6f8d68da53 | |
| Step 9/29 : RUN npm install generic-filehandle | |
| ---> Running in 59b40f392d0b | |
| npm notice created a lockfile as package-lock.json. You should commit this file. | |
| + [email protected] | |
| added 5 packages from 5 contributors and audited 5 packages in 0.604s | |
| found 0 vulnerabilities |
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| CDS:VC2010_MAPPED_K10F12.5 | |
| Transcript:VC2010_tRNA_RF00005_505 | |
| CDS:VC2010_MAPPED_C24A1.4 | |
| Transcript:VC2010_ceN110_RF01614_985 | |
| Transcript:VC2010_ceN110_RF01614_984 | |
| CDS:VC2010_MAPPED_Y71D11A.4 | |
| Transcript:VC2010_tRNA_RF00005_91 | |
| Transcript:VC2010_tRNA_RF00005_92 | |
| Transcript:VC2010_tRNA_RF00005_93 | |
| CDS:VC2010_MAPPED_Y119D3A.5 |
scottcain
/ dynamically inserting jbrowse into a div
Created
August 20, 2019 23:47
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| <a href="http://jbrowse.alliancegenome.org/jbrowse/index.html?data=data%2FHomo%20sapiens&tracks=All%20Genes&highlight=&lookupSymbol=CFTR&loc=7%3A117366917..117782061">Human</a> | |
| <div id="jbrowse_human" class="jbrowse-view-iframe" | |
| style="width:100%;height:400px;background-color:#fff;resize: vertical;overflow: auto;" | |
| onrsize="resizeJBrowse();">Hmm, jbrowse failed to load :-(</div> | |
| <script type="text/javascript"> | |
| //this is the trick--setting the innerHTML to an object that consists of what will be a jbrowse div once jbrowse runs | |
| document.getElementById("jbrowse_human").innerHTML='<object id="innerJBrowse" type="text/html" style="width:100%;height:400px;overflow: auto;" data="http://jbrowse.alliancegenome.org/jbrowse/index.html?data=data%2FHomo%20sapiens&tracks=All%20Genes&highlight=&lookupSymbol=CFTR&loc=7%3A117366917..117782061&nav=0&tracklist=0&overview=0" ></object>'; | |
| </script> | |
| <a href="http://jbrowse.alliancegenome.org/jbrowse/index.html?data=data%2FMus%20musculus&tracks=All%20Genes&highlight |
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| I Variation_project_Polymorphism SNP 7110119 7110119 . + . _Variation=WBVar01432033;_Polymorphism=1;Name=WBVar01432033;_Substitution=A/T;_Strain=function values() { [native code] };_Public_name=WBVar01432033 | |
| ### | |
| I Variation_project_Polymorphism SNP 7110177 7110177 . + . _Variation=WBVar01283442;_Polymorphism=1;Name=WBVar01283442;_Other_name=cewivar00505922;_Substitution=T/A;_Strain=function values() { [native code] };_Public_name=WBVar01283442 | |
| I Variation_project_Polymorphism SNP 7110740 7110740 . + . _Variation=WBVar00154168;_Consequence=Intron;_Polymorphism=1;Name=WBVar00154168;_Other_name=function values() { [native code] };_Substitution=G/C;_Strain=function values() { [native code] };_Public_name=WBVar00154168 | |
| ### | |
| I Variation_project_Polymorphism SNP 7112790 7112790 . + . _Variation=WBVar01283444;_Polymorphism=1;Name=WBVar01283444;_Other_name=cewivar00505923;_Substitution=G/T;_Strain=JU258;_Public_name=WBVar01283444 | |
| I Variation_project_Polymorphism deletion 7112907 7112911 . + . _Variation=WBVar02039717;_ |
scottcain
/ elegans_B0304.1c.1_transcript_gff
Last active
January 8, 2019 23:07
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| II WormBase mRNA 4518560 4522523 . + . ID=Transcript:B0304.1c.1;Parent=Gene:WBGene00001948;Name=B0304.1c.1;wormpep=CE30067;locus=hlh-1 | |
| II WormBase five_prime_UTR 4518560 4518622 . + . Parent=Transcript:B0304.1c.1 | |
| II WormBase exon 4518560 4518622 . + . Parent=Transcript:B0304.1c.1 | |
| II WormBase intron 4518623 4519064 . + . Parent=Transcript:B0304.1c.1 | |
| II WormBase five_prime_UTR 4519065 4519068 . + . Parent=Transcript:B0304.1c.1 | |
| II WormBase exon 4519065 4519238 . + . Parent=Transcript:B0304.1c.1 | |
| II WormBase CDS 4519069 4519238 . + 0 ID=CDS:B0304.1c;Parent=Transcript:B0304.1c.1,Transcript:B0304.1c.2;Name=B0304.1c;prediction_status=Partially_confirmed;wormpep=CE30067;protein_id=CCD61733.1;locus=hlh-1 | |
| II WormBase CDS 4520949 4521226 . + 1 ID=CDS:B0304.1c;Parent=Transcript:B0304.1c.1,Transcript:B0304.1c.2;Name=B0304.1c;prediction_status=Partially_confirmed;wormpep=CE30067;protein_id=CCD61733.1;locus=hlh-1 | |
| II WormBase CDS 4521267 4521541 . + 2 ID=CDS:B0304.1c;Parent=Transcript:B0304.1c.1,Transcript:B0304.1c.2;Name=B03 |
scottcain
/ filter_flybase_fasta.pl
Created
September 20, 2017 15:22
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| #!/usr/bin/perl | |
| use strict; | |
| use warnings; | |
| use Bio::DB::Fasta; | |
| use Bio::SeqIO; | |
| my $db = Bio::DB::Fasta->new('dmel-all-chromosome-r6.13.fasta'); | |
| my $out = Bio::SeqIO->new(-file => "out.fasta", -format => 'fasta'); |
scottcain
/ Wormbase landmark.gff
Created
July 17, 2017 16:10
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| I landmark gene 146486 154850 . - . ID=landmark:bli-3;locus=bli-3 | |
| I landmark gene 1176471 1190829 . + . ID=landmark:smg-2;locus=smg-2 | |
| I landmark gene 2706883 2717549 . + . ID=landmark:lin-17;locus=lin-17 | |
| I landmark gene 3798566 3805737 . - . ID=landmark:unc-11;locus=unc-11 | |
| I landmark gene 4675135 4679409 . + . ID=landmark:unc-57;locus=unc-57 | |
| I landmark gene 5432158 5433054 . - . ID=landmark:dpy-5;locus=dpy-5 | |
| I landmark gene 6342231 6356678 . + . ID=landmark:bli-4;locus=bli-4 | |
| I landmark gene 7422785 7454088 . + . ID=landmark:unc-13;locus=unc-13 | |
| I landmark gene 8897613 8901435 . - . ID=landmark:unc-29;locus=unc-29 | |
| I landmark gene 8928748 8931089 . + . ID=landmark:tsp-15;locus=tsp-15 |