Commit 2ffe3588 authored by sauloal's avatar sauloal
Browse files

add html

parent d26ea393
<html>
<head>
<meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1">
</head>
<body>
<div style="position:absolute; left: 0; right: 0; bottom: 0; top: 0px;">
<iframe id="jframe" width="100%" height="100%" frameborder="0" style="margin: 0; padding: 0; height: 100%; overflow: hidden;"></iframe>
</div>
</body>
<footer>
<script src="urls.js?v3"></script>
<script>
console.log("src : ", src );
console.log("stores: ", stores);
console.log("tracks: ", tracks);
console.log(JSON.stringify(stores))
console.log(JSON.stringify(tracks))
var jurl = src + "&addStores=" + JSON.stringify(stores) + "&addTracks=" + JSON.stringify(tracks);
console.log("jurl:" + jurl );
//document.getElementById("jframe").src = jurl;
//var win = window.open(jurl, '_blank');
//win.focus();
window.location.href = jurl;
</script>
</footer>
</html>
var src = "http://solgenomics.net/jbrowse/current/?data=data%2Fjson%2FSL2.50";
var gff_file_type = "JBrowse/Store/SeqFeature/GFF3";
var glyph_canvas = "JBrowse/View/Track/CanvasFeatures";
var data = [
// name label file_type glyph_type file_url
["om_all" , "om_all" , gff_file_type, glyph_canvas, "https://dl.dropboxusercontent.com/u/753166/S_lycopersicum_chromosomes.2.50.BspQI_to_EXP_REFINEFINAL1_xmap.txt.augmented.tsv.gff3"],
["om_conf10" , "om_conf10" , gff_file_type, glyph_canvas, "https://dl.dropboxusercontent.com/u/753166/S_lycopersicum_chromosomes.2.50.BspQI_to_EXP_REFINEFINAL1_xmap.txt.augmented.tsv_Confidence_ge_10.report.tsv.gff3"],
["om_conf10_broken", "om_conf10_broken", gff_file_type, glyph_canvas, "https://dl.dropboxusercontent.com/u/753166/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" , "Ns" , gff_file_type, glyph_canvas, "https://dl.dropboxusercontent.com/u/753166/S_lycopersicum_chromosomes.2.50.fa.gff3"],
["Contigs" , "Contigs" , gff_file_type, glyph_canvas, "https://dl.dropboxusercontent.com/u/753166/SL2.50ch_from_sc.agp.gff3.contig.gff3"],
["Gaps" , "Gaps" , gff_file_type, glyph_canvas, "https://dl.dropboxusercontent.com/u/753166/SL2.50ch_from_sc.agp.gff3.gap.gff3"],
["Scaffolds" , "Scaffolds" , gff_file_type, glyph_canvas, "https://dl.dropboxusercontent.com/u/753166/SL2.50ch_from_sc.agp.gff3.scaffold.gff3"]
];
var stores = {};
var tracks = [];
for ( var dpos in data ) {
var datal = data[dpos];
var name = datal[0];
var label = datal[1];
var file_type = datal[2];
var glyph_type = datal[3];
var file_url = datal[4];
console.log("name: "+name+" label: "+label+" file_type: "+file_type+" glyph_type: "+glyph_type+" file_url: "+file_url);
stores[name] = { "type": file_type, "urlTemplate": file_url };
tracks.push({
"label": label,
"store": name,
"type" : glyph_type
});
}
// addStores={"url":{"type":"JBrowse/Store/SeqFeature/GFF3","urlTemplate":"http://assembly.ab.wurnet.nl/~aflit001/jbrowse/data/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"}}&addTracks=[{"label":"genes","type":"JBrowse/View/Track/CanvasFeatures","store":"url"}]
// addStores={"url":{"type":"JBrowse/Store/SeqFeature/GFF3","urlTemplate":"https://db.tt/UWgVtjvh"}}&addTracks=[{"label":"genes","type":"JBrowse/View/Track/CanvasFeatures","store":"url"}]
// addStores={"url":{"type":"JBrowse/Store/SeqFeature/GFF3","urlTemplate":"https://dl.dropboxusercontent.com/u/753166/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"}}&addTracks=[{"label":"genes","type":"JBrowse/View/Track/CanvasFeatures","store":"url"}]
......@@ -20,7 +20,7 @@ if [[ ! -f "$filtered" ]]; then
./om_filter.py $augmented --filter Confidence:ge:10 --filter _meta_num_orientations:gt:1 --filter _meta_is_max_confidence_for_qry_chrom:eq:T
fi
exit 0
#exit 0
#rm $delta || true
if [[ ! -f "$delta" ]]; then
./om_to_delta.py $filtered
......@@ -33,10 +33,10 @@ if [[ ! -f "$gff" ]]; then
fi
#./om_filter.py $augmented --filter Confidence:ge:10
#./om_filter.py $augmented --filter Confidence:ge:10 --filter _meta_num_qry_matches:gt:1
./om_filter.py $augmented --filter Confidence:ge:10
./om_filter.py $augmented --filter Confidence:ge:10 --filter _meta_num_qry_matches:gt:1
#./om_to_gff.py ${augmented} --names-from-file $chromosome_names --exclude-cols-from-file $cols_to_escape
#./om_to_gff.py ${augmented}_Confidence_ge_10.report.tsv --names-from-file $chromosome_names --exclude-cols-from-file $cols_to_escape
./om_to_gff.py ${augmented} --names-from-file $chromosome_names --exclude-cols-from-file $cols_to_escape
./om_to_gff.py ${augmented}_Confidence_ge_10.report.tsv --names-from-file $chromosome_names --exclude-cols-from-file $cols_to_escape
./om_to_delta.py ${augmented}_Confidence_ge_10__meta_num_qry_matches_gt_1.report.tsv
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