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Commit e49a3ec4 authored by Bertrand NÉRON's avatar Bertrand NÉRON
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rename secreton into txssdb

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src/couchapp/secreton/.couchappignore deleted 100644 → 0
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[
// filenames matching these regexps will not be pushed to the database
// uncomment to activate; separate entries with ","
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// ".*\\.bak$"
"\\.project" ,
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src/couchapp/secreton/README.md deleted 100644 → 0
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## Generated CouchApp
This is meant to be an example CouchApp and to ship with most of the CouchApp goodies.
Clone with git:
git clone git://github.com/couchapp/example.git
cd example
Install with
couchapp push . http://localhost:5984/example
or (if you have security turned on)
couchapp push . http://adminname:adminpass@localhost:5984/example
You can also create this app by running
couchapp generate example && cd example
couchapp push . http://localhost:5984/example
Deprecated: *couchapp generate proto && cd proto*
## Todo
* factor CouchApp Commonjs to jquery.couch.require.js
* use $.couch.app in app.js
## License
Apache 2.0
src/couchapp/secreton/_attachments/images/systeme_simple.svg deleted 100644 → 0
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src/couchapp/secreton/_attachments/index.html deleted 100644 → 0
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<!DOCTYPE html>
<html>
<head>
<title>Secreton</title>
<link rel="stylesheet" href="style/main.css" type="text/css">
<link rel="stylesheet" href="style/tooltip.css" type="text/css">
<link rel="stylesheet" href="style/smoothness/jquery-ui-1.8.17.custom.css" type="text/css">
<script src="/_utils/script/jquery.js"></script>
<!-- <script src="/_utils/script/jquery-ui-1.8.11.custom.min.js"></script>-->
<script src="script/jquery-ui-1.8.17.custom.min.js"></script>
</head>
<body>
<h1>Secreton</h1>
<h2>Non-Flagellar Type III Secretion Systems in sequenced genomes</h2>
<div id="head">
<img src="images/systeme_complet.png" title="Non-Flagellar Type III Secretion System schema" alt="Non-Flagellar Type III Secretion System schema">
<p>Non-Flagellar Type III Secretion Systems (NF-T3SS, or injectisomes) are bacterial machineries partially homologous to the bacterial flagellum,
which allow direct injection of bacterial effectors from bacterial cytoplasm to eukaryotic cells via a molecular needle (cf. schema above).
NF-T3SS are found in animal and plant pathogens (<span class="gene_name">Yersinia pestis</span>,<span class="gene_name">Escherichia coli</span>, <span class="gene_name">Burkholderia</span>,...),
but also in plant and insect symbionts (e.g., Rhizobiales).</p>
<p>This website allows to query a dataset of 216 NF-T3SS retrieved from 1385 complete genome sequences.
These systems were detected with proteic profiles of NF-T3SS core genes (<span class="gene_name">sctC</span>, <span class="gene_name">sctN</span>, <span class="gene_name">sctJ</span>,
<span class="gene_name">sctQ</span>, <span class="gene_name">sctR</span>, <span class="gene_name">sctS</span>, <span class="gene_name">sctT</span>,
<span class="gene_name">sctU</span>, <span class="gene_name">sctV</span>),
and with an analysis of the genomic context of the hits obtained.
This dataset along with the methodology is described in <a href="http://www.plosgenetics.org/doi/pgen.1002983">Abby and Rocha 2012</a>.</p>
<p>Proteic profiles used for this study are available to analyze user data on the
Mobyle web server: <a href="http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::T3SSscan-FLAGscan" target="_blank">http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::T3SSscan-FLAGscan</a>.
These profiles allow to detect both NF-T3SS and flagella.</p>
<div class="citation">
Citation: <span class="citation_author">Abby SS</span>,
<span class="citation_author">Rocha EPC </span>
<span class="citation_date">(2012)</span>
<a href="http://www.plosgenetics.org/doi/pgen.1002983" target="_blank"><span class="citation_article_title">The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems.</span></a>
<span class="citation_journal_title">PLoS Genet</span>
<span class="citation_issue"> 8(9):</span>
<span class="citation_start_page">e1002983.</span>
</div>
</div>
<div id="request">
<form>
<fieldset>
<legend>Detected NF-T3SS can be queried: </legend>
<label for="taxidSearch">by replicon taxon id (ex:155864)
<input type="text" name="taxidSearch" id="taxidInput" class="ui-widget ui-corner-all" />
<button type="button" id="taxidButton">search by taxid</button>
</label>
<label for="strainSearch">by strain <span style="font-size:smaller; font-style:italic;">(enter at least 3 characters)</span>
<input type="text" name="strainSearch" id="strainInput" size="100" class="ui-widget ui-corner-all" />
</label>
<label for="taxonomySearch">by taxonomy <span style="font-size:smaller; font-style:italic;">(enter at least 3 characters)</span>
<input type="text" name="taxonomySearch" id="taxonomyInput" size="50" class="ui-widget ui-corner-all" />
</label>
<label for="famillySearch">by T3SS family
<select name="familySearch" id="familyList" class="ui-widget ui-corner-all ui-state-default"> </select>
</label>
<label for="nameSearch">by replicon name (ex:BUMA001c02)
<input type="text" name="nameSearch" id="nameInput"class="ui-widget ui-corner-all" />
<select name="queryType" id="nameQueryType"class="ui-widget ui-corner-all ui-state-default">
<option value="is" selected="selected" class="ui-widget ui-corner-all ">is</option>
<option value="start_with" class="ui-widget ui-corner-all ">start_with</option>
</select>
<button type="button" id="nameButton">search by name</button>
</label>
</fieldset>
</form>
</div>
<div id="results"></div>
<div id="footer">
Visit our website: <a href="http://www.pasteur.fr/ip/easysite/pasteur/en/research/scientific-departments/genomes-and-genetics/units-and-groups/evolutionary-microbial-genomics/index">Microbial evolutionary genomics group</a>
</div>
</body>
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$(".tooltip a" , "#results").live('mouseenter', function(){
var link$ = $(this);
timer = setTimeout(function(){
var pos = link$.position();
var top = pos.top + link$.outerHeight(true)+3;
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500);
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clearTimeout(timer);
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var get_results = function( view , args ){
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args.limit= 45+1;
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}
$("#nameButton").click( function(){
var params = {};
var $query= $("#nameQueryType").attr("value")
if ( $query == "start_with" ){
var key= $.trim($("#nameInput").attr("value"));
if( key ){
params.startkey='"'+key+'"';
params.endkey='"'+key+'\uFFFF"';
params.query_type="start_with";
}
}else{
var key= $("#nameInput").attr("value");
if( key ){ params.key='"'+key+'"'}
}
get_results( 'by_replicon_name', params);
});
$("#nameInput").keypress(function(event){
if(event.which == 13){
$("#nameButton").click();
}
});
$("#taxidButton").click( function(){
var params = {};
var key= $.trim($("#taxidInput").attr("value"));
if( key ){
if ( /^\d+$/.test( key )){
params.key = key ;
} else{
$("#results").html( '<ul>Invalid taxon id:'+key+'</ul>');
return ;
}
}
get_results( 'by_replicon_taxid', params);
});
$("#taxidInput").keypress(function(event){
if(event.which == 13){
$("#taxidButton").click();
}
});
$("#familyButton").click( function(){
var params = {};
var key= $.trim($("#familyInput").attr("value"));
if( key ){ params.key='"'+key+'"'}
get_results( 'by_family', $.param(params));
});
$.getJSON( "_view/t3ss_family" , {group:true}, function(response){
var html = '<option value="" class="ui-widget ui-corner-all ui-widget-content">choose a T3SS Family</option>\n';
for ( var i=0 ; i< response.rows.length ; i++){
html = html+'<option value="'+response.rows[i].key+'" class="ui-widget ui-corner-all">'+response.rows[i].key+'</option>\n';
}
$("#familyList").html( html );
$("#familyList").change(function(event){
var opt_value = $(event.target).val();
if ( opt_value){
var params = {};
params.key='"'+opt_value+'"'
get_results( 'by_family', params );
}else{
$("#results div").remove();
}
});
});
$("#strainInput").autocomplete({
source: function(req , response){
var term = '"'+$.trim(req.term).toLowerCase()+'"';
var suggestions =[];
$.getJSON("_view/strain", {key:term} , function(suggested_strain){
var cur_value ;
for(var i =0; i<suggested_strain.rows.length; i++){
if (cur_value != suggested_strain.rows[i].value){
suggestions.push(suggested_strain.rows[i].value);
cur_value = suggested_strain.rows[i].value;
}
}
response(suggestions);
});
},
select: function(evt , ui ){
strain= ui.item.value ;
params = { key: '"'+strain+'"' };
get_results( 'by_replicon_strain', params);
},
minLength:3
});
$("#strainInput").click( function (evt){
$("#results div").remove();
});
$("#strainInput").keypress(function(event){
if(event.which == 13){
strain= $(this).attr("value");
params = { key: '"'+strain+'"' };
get_results( 'by_replicon_strain', params);
}
});
$("#taxonomyInput").autocomplete({
source: function(req , response){
var term = '"'+req.term.toLowerCase()+'"';
var params= {
group:true,
startkey:'['+term+']',
endkey:'['+term+',{}]'
};
var suggestions =[];
$.getJSON("_view/taxonomy_terms", params , function(suggested_term){
for(var i =0; i<suggested_term.rows.length; i++){
suggestions.push(suggested_term.rows[i].key[1]);
}
response(suggestions);
});
},
select: function(evt , ui ){