Commit 4ec68a5f authored by sauloal's avatar sauloal
Browse files

ipython

parent ce9a2581
Pipeline #398 skipped
......@@ -10,7 +10,7 @@
-->
</body>
<footer>
<script src="urls.js?v5"></script>
<script src="urls.js?v6"></script>
<script>
console.log("src : ", src );
console.log("stores: ", stores);
......@@ -19,7 +19,7 @@
console.log(JSON.stringify(stores))
console.log(JSON.stringify(tracks))
var jurl = src + "&addStores=" + JSON.stringify(stores) + "&addTracks=" + JSON.stringify(tracks) + '&variables={"vt":"_T"}';
var jurl = src + "&addStores=" + JSON.stringify(stores) + "&addTracks=" + JSON.stringify(tracks);
console.log("jurl:" + jurl );
//document.getElementById("jframe").src = jurl;
......
......@@ -4,6 +4,7 @@ var glyph_canvas = "JBrowse/View/Track/CanvasFeatures";
var glyph_align = "JBrowse/View/Track/Alignments2";
//var glyph_canvas = "JBrowse/View/Track/Alignments2";
var dropbox_url = "https://dl.dropboxusercontent.com/u/753166/jbrowse/";
var ext = '.gff3'
var color1 = "red";
var color2 = "green";
......@@ -12,52 +13,60 @@ var color4 = "purple";
var color5 = "black";
var data = [
// name file_type glyph_type color file_url
["OM all" , gff_file_type, glyph_canvas, color1, dropbox_url+"S_lycopersicum_chromosomes.2.50.BspQI_to_EXP_REFINEFINAL1_xmap.txt.augmented.tsv.gff3"],
["OM conf10" , gff_file_type, glyph_canvas, color1, dropbox_url+"S_lycopersicum_chromosomes.2.50.BspQI_to_EXP_REFINEFINAL1_xmap.txt.augmented.tsv_Confidence_ge_10.report.tsv.gff3"],
["OM conf10 broken" , gff_file_type, glyph_canvas, color1, dropbox_url+"S_lycopersicum_chromosomes.2.50.BspQI_to_EXP_REFINEFINAL1_xmap.txt.augmented.tsv_Confidence_ge_10__meta_num_orientations_gt_1__meta_is_max_confidence_for_qry_chrom_eq_T.report.tsv.gff3"],
// name file_type glyph_type color file_url
//aggressive QUAL > 200
//["gbrowse repeats aggressive All" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats_aggressive.gff3"],
//["gbrowse repeats aggressive All PGSC" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats_aggressive.gff3.PGSC.gff3"],
//["gbrowse repeats aggressive All scaffold", gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats_aggressive.gff3.scaffold.gff3"],
//["gbrowse repeats aggressive Copia" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats_aggressive.gff3.Copia.gff3"],
//["gbrowse repeats aggressive Gypsy" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats_aggressive.gff3.Gypsy.gff3"],
//["gbrowse repeats aggressive others" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats_aggressive.gff3.others.gff3"],
//["gbrowse repeats aggressive SINE" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats_aggressive.gff3.SINE.gff3"],
//["gbrowse repeats All" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats.gff3"],
//["gbrowse repeats All PGSC" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats.gff3.PGSC.gff3"],
//["gbrowse repeats All scaffold" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats.gff3.scaffold.gff3"],
//["gbrowse repeats Copia" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats.gff3.Copia.gff3"],
//["gbrowse repeats Gypsy" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats.gff3.Gypsy.gff3"],
//["gbrowse repeats others" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats.gff3.others.gff3"],
//["gbrowse repeats SINE" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats.gff3.SINE.gff3"],
//["gbrowse repeats All" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats.gff3" ],
["gbrowse repeats Copia" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats.gff3.Copia.gff3" ],
["gbrowse repeats Gypsy" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats.gff3.Gypsy.gff3" ],
["gbrowse repeats others" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats.gff3.others.gff3" ],
//["gbrowse repeats All PGSC" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats.gff3.PGSC.gff3" ],
["gbrowse repeats All scaffold" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats.gff3.scaffold.gff3" ],
//["gbrowse repeats SINE" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats.gff3.SINE.gff3" ],
//aggressive QUAL < 200
//["gbrowse repeats aggressive All" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats_aggressive.gff3" ],
["gbrowse repeats aggressive Copia" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats_aggressive.gff3.Copia.gff3" ],
["gbrowse repeats aggressive Gypsy" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats_aggressive.gff3.Gypsy.gff3" ],
["gbrowse repeats aggressive others" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats_aggressive.gff3.others.gff3" ],
//["gbrowse repeats aggressive All PGSC" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats_aggressive.gff3.PGSC.gff3" ],
["gbrowse repeats aggressive All scaffold", gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats_aggressive.gff3.scaffold.gff3"],
//["gbrowse repeats aggressive SINE" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_repeats_aggressive.gff3.SINE.gff3" ],
//["gbrowse BAC All" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_SL_BAC.gff3" ],
//["gbrowse BAC clone" , gff_file_type, glyph_align , color1, dropbox_url+"gbrowse_SL_BAC.gff3.BAC_clone.gff3" ],
//["gbrowse BAC end" , gff_file_type, glyph_align , color1, dropbox_url+"gbrowse_SL_BAC.gff3.BAC_end.gff3" ],
//["gbrowse BAC problematic All" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_SL_BAC_f.gff3" ],
//["gbrowse BAC clone problematic " , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_SL_BAC_f.gff3.BAC_clone.gff3" ],
//["gbrowse BAC end problematic" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_SL_BAC_f.gff3.BAC_end.gff3" ],
//["gbrowse BAC problematic All" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_SL_BAC_f.gff3"],
//["gbrowse BAC clone problematic " , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_SL_BAC_f.gff3.BAC_clone.gff3"],
//["gbrowse BAC end problematic" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_SL_BAC_f.gff3.BAC_end.gff3"],
//["gbrowse BAC All" , gff_file_type, glyph_canvas, color1, dropbox_url+"gbrowse_SL_BAC.gff3"],
//["gbrowse BAC clone" , gff_file_type, glyph_align, color1, dropbox_url+"gbrowse_SL_BAC.gff3.BAC_clone.gff3"],
//["gbrowse BAC end" , gff_file_type, glyph_align, color1, dropbox_url+"gbrowse_SL_BAC.gff3.BAC_end.gff3"],
//["assembly" , gff_file_type, glyph_canvas, color1, dropbox_url+"ITAG2.4_assembly.gff3"],
["assembly contigs" , gff_file_type, glyph_align , color2, dropbox_url+"ITAG2.4_assembly.gff3.contig.gff3"],
["assembly scaffolds" , gff_file_type, glyph_align , color2, dropbox_url+"ITAG2.4_assembly.gff3.supercontig.gff3"],
//["assembly gaps" , gff_file_type, glyph_align , color2, dropbox_url+"ITAG2.4_assembly.gff3.remark.gff3"],
//["agp All" , gff_file_type, glyph_canvas, color1, dropbox_url+"SL2.50ch_from_sc.agp.gff3"],
//["agp contig" , gff_file_type, glyph_canvas, color1, dropbox_url+"SL2.50ch_from_sc.agp.gff3.contig.gff3"],
["agp gap" , gff_file_type, glyph_align , color2, dropbox_url+"SL2.50ch_from_sc.agp.gff3.gap.gff3"],
//["agp scaffold" , gff_file_type, glyph_canvas, color1, dropbox_url+"SL2.50ch_from_sc.agp.gff3.scaffold.gff3"],
//["BAC All" , gff_file_type, glyph_canvas, color3, dropbox_url+"ITAG2.4_genomic_reagents.gff3"],
["BAC clone" , gff_file_type, glyph_align , color3, dropbox_url+"ITAG2.4_genomic_reagents.gff3.BAC_clone.gff3"],
//["BAC end" , gff_file_type, glyph_align , color3, dropbox_url+"ITAG2.4_genomic_reagents.gff3.BAC_end.gff3"],
//["repeats All" , gff_file_type, glyph_canvas, color4, dropbox_url+"ITAG2.4_repeats.gff3"],
["repeats PGSC" , gff_file_type, glyph_canvas, color4, dropbox_url+"ITAG2.4_repeats.gff3.PGSC.gff3"],
["repeats scaffold" , gff_file_type, glyph_canvas, color4, dropbox_url+"ITAG2.4_repeats.gff3.scaffold.gff3"],
//["repeats Copia" , gff_file_type, glyph_align , color4, dropbox_url+"ITAG2.4_repeats.gff3.Copia.gff3"],
//["repeats Gypsy" , gff_file_type, glyph_align , color4, dropbox_url+"ITAG2.4_repeats.gff3.Gypsy.gff3"],
//["repeats others" , gff_file_type, glyph_align , color4, dropbox_url+"ITAG2.4_repeats.gff3.others.gff3"],
//["repeats SINE" , gff_file_type, glyph_align , color4, dropbox_url+"ITAG2.4_repeats.gff3.SINE.gff3"],
["Ns" , gff_file_type, glyph_align , color5, dropbox_url+"S_lycopersicum_chromosomes.2.50.fa.gff3"]
//["assembly" , gff_file_type, glyph_canvas, color1, dropbox_url+"ITAG2.4_assembly.gff3" ],
["assembly contigs" , gff_file_type, glyph_align , color2, dropbox_url+"ITAG2.4_assembly.gff3.contig.gff3" ],
//["assembly gaps" , gff_file_type, glyph_align , color2, dropbox_url+"ITAG2.4_assembly.gff3.remark.gff3" ],
["assembly scaffolds" , gff_file_type, glyph_align , color2, dropbox_url+"ITAG2.4_assembly.gff3.supercontig.gff3" ],
//["BAC All" , gff_file_type, glyph_canvas, color3, dropbox_url+"ITAG2.4_genomic_reagents.gff3" ],
["BAC clone" , gff_file_type, glyph_align , color3, dropbox_url+"ITAG2.4_genomic_reagents.gff3.BAC_clone.gff3" ],
//["BAC end" , gff_file_type, glyph_align , color3, dropbox_url+"ITAG2.4_genomic_reagents.gff3.BAC_end.gff3" ],
//["repeats All" , gff_file_type, glyph_canvas, color4, dropbox_url+"ITAG2.4_repeats.gff3" ],
//["repeats Copia" , gff_file_type, glyph_align , color4, dropbox_url+"ITAG2.4_repeats.gff3.Copia.gff3" ],
//["repeats Gypsy" , gff_file_type, glyph_align , color4, dropbox_url+"ITAG2.4_repeats.gff3.Gypsy.gff3" ],
//["repeats others" , gff_file_type, glyph_align , color4, dropbox_url+"ITAG2.4_repeats.gff3.others.gff3" ],
//["repeats PGSC" , gff_file_type, glyph_canvas, color4, dropbox_url+"ITAG2.4_repeats.gff3.PGSC.gff3" ],
//["repeats scaffold" , gff_file_type, glyph_canvas, color4, dropbox_url+"ITAG2.4_repeats.gff3.scaffold.gff3" ],
//["repeats SINE" , gff_file_type, glyph_align , color4, dropbox_url+"ITAG2.4_repeats.gff3.SINE.gff3" ],
["OM all" , gff_file_type, glyph_canvas, color1, dropbox_url+"S_lycopersicum_chromosomes.2.50.BspQI_to_EXP_REFINEFINAL1_xmap.txt.augmented.tsv.gff3"],
["OM conf10" , gff_file_type, glyph_canvas, color1, dropbox_url+"S_lycopersicum_chromosomes.2.50.BspQI_to_EXP_REFINEFINAL1_xmap.txt.augmented.tsv_Confidence_ge_10.report.tsv.gff3"],
["OM conf10 broken" , gff_file_type, glyph_canvas, color1, dropbox_url+"S_lycopersicum_chromosomes.2.50.BspQI_to_EXP_REFINEFINAL1_xmap.txt.augmented.tsv_Confidence_ge_10__meta_num_orientations_gt_1__meta_is_max_confidence_for_qry_chrom_eq_T.report.tsv.gff3"],
["Ns" , gff_file_type, glyph_align , color5, dropbox_url+"S_lycopersicum_chromosomes.2.50.fa.gff3" ],
//["agp All" , gff_file_type, glyph_canvas, color1, dropbox_url+"SL2.50ch_from_sc.agp.gff3" ],
//["agp contig" , gff_file_type, glyph_canvas, color1, dropbox_url+"SL2.50ch_from_sc.agp.gff3.contig.gff3" ],
["agp gap" , gff_file_type, glyph_align , color2, dropbox_url+"SL2.50ch_from_sc.agp.gff3.gap.gff3" ],
//["agp scaffold" , gff_file_type, glyph_canvas, color1, dropbox_url+"SL2.50ch_from_sc.agp.gff3.scaffold.gff3" ],
];
......@@ -75,16 +84,19 @@ var data = [
var stores = {};
var tracks = [];
for ( var dpos in data ) {
var datal = data[dpos];
var name = datal[0];
var file_type = datal[1];
var glyph_type = datal[2];
var color = datal[3];
var file_url = datal[4];
console.log("name: "+name+" file_type: "+file_type+" glyph_type: "+glyph_type+" color: "+color+" file_url: "+file_url);
var datal = data[dpos];
var name = datal[0];
var file_type = datal[1];
var glyph_type = datal[2];
var color = datal[3];
var file_url = datal[4];
var filenum = parseInt(dpos)+1;
var file_url_small = dropbox_url+'small/'+filenum+ext;
console.log("name: "+name+" file_type: "+file_type+" glyph_type: "+glyph_type+" color: "+color+" file_url_small: "+file_url_small+" file_url: "+file_url);
var s_name = "s" + dpos;
stores[s_name] = { "type": file_type, "urlTemplate": file_url };
var s_name = "s" + dpos;
stores[s_name] = { "type": file_type, "urlTemplate": file_url_small };
tracks.push({
"label": name,
"store": s_name,
......
.ipynb_checkpoints
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