Mercurial > repos > eduardo > annotateviz
changeset 4:92921dfea0b5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 230f5fe14cc469e56626201a5c377686976d81fc
| author | eduardo |
|---|---|
| date | Sat, 24 Jun 2017 14:55:25 -0400 |
| parents | 3302f18f9e16 |
| children | 9cc97d18dff1 |
| files | annotateviz.py annotateviz.xml prediction.json static/js/editgff.js static/js/gff_app.js static/trinotateviz.html test-data/gff.json |
| diffstat | 7 files changed, 120 insertions(+), 11 deletions(-) [+] |
line wrap: on
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--- a/annotateviz.py Sat Jun 17 15:10:53 2017 -0400 +++ b/annotateviz.py Sat Jun 24 14:55:25 2017 -0400 @@ -18,7 +18,8 @@ argv.append("-h") parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter, description=__doc__) parser.add_argument('-d','--database', help="gffutils sqlite database") - parser.add_argument('-j','--json', help="report in json format") + parser.add_argument('-j','--json', help="annotations in json format") + parser.add_argument('-p','--pred', help="predictions in json") args = parser.parse_args(argv) gffutils.constants.always_return_list = False db = gffutils.interface.FeatureDB(args.database) @@ -29,5 +30,34 @@ add_matches(db.features_of_type("PFAM"), prediction_list) fout=open(args.json, 'w') json.dump(prediction_list,fout) + # create json for protein predictions + array=[] + for f in db.features_of_type("gene"): + dict = {} + dict['seqid'] = f.seqid + dict['source'] = f.source + dict['featuretype'] = f.featuretype + dict['start'] = f.start + dict['end'] = f.end + dict['score'] = f.score + dict['strand'] = f.strand + dict['frame'] = f.frame + dict['attributes']=f.attributes.__dict__["_d"] + array.append(dict) + for c in db.children(f): + dict = {} + dict['seqid'] = c.seqid + dict['source'] = c.source + dict['featuretype'] = c.featuretype + dict['start'] = c.start + dict['end'] = c.end + dict['score'] = c.score + dict['strand'] = c.strand + dict['frame'] = c.frame + dict['attributes'] = c.attributes.__dict__["_d"] + array.append(dict) + fout2=open(args.pred,'w') + json.dump(array,fout2) + if __name__ == "__main__": main(sys.argv[1:],sys.stdout)
--- a/annotateviz.xml Sat Jun 17 15:10:53 2017 -0400 +++ b/annotateviz.xml Sat Jun 24 14:55:25 2017 -0400 @@ -14,9 +14,10 @@ --outdir $output.files_path $trackxml && ## $output.files_path/index.html $output; -python $__tool_directory__/annotateviz.py -d $db -j ${output.files_path}/trans.json && +python $__tool_directory__/annotateviz.py -d $db -j ${output.files_path}/trans.json -p ${output.files_path}/gff.json && sed "s@input_db@${__app__.security.encode_id($db.id)}@" $__tool_directory__/static/trinotateviz.html > $output && cp $__tool_directory__/static/js/gff_app.js ${output.files_path} && +cp $__tool_directory__/static/js/edit.js ${output.files_path} && cp $__tool_directory__/static/css/main.css ${output.files_path}; ]]></command> <configfiles>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/prediction.json Sat Jun 24 14:55:25 2017 -0400 @@ -0,0 +1,1 @@ +[{"featuretype": "gene", "end": 344, "score": ".", "start": 1, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN5404_c0_g1_i1", "attributes": {"ID": ["TRINITY_DN5404_c0_g1_i1|g.6938"], "Name": ["ORF%20TRINITY_DN5404_c0_g1_i1%7Cg.6938%20TRINITY_DN5404_c0_g1_i1%7Cm.6938%20type%3Ainternal%20len%3A115%20%28-%29"]}, "strand": "-"}, {"featuretype": "mRNA", "end": 344, "score": ".", "start": 1, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN5404_c0_g1_i1", "attributes": {"ID": ["TRINITY_DN5404_c0_g1_i1|m.6938"], "Parent": ["TRINITY_DN5404_c0_g1_i1|g.6938"], "Name": ["ORF%20TRINITY_DN5404_c0_g1_i1%7Cg.6938%20TRINITY_DN5404_c0_g1_i1%7Cm.6938%20type%3Ainternal%20len%3A115%20%28-%29"]}, "strand": "-"}, {"featuretype": "five_prime_UTR", "end": 344, "score": ".", "start": 343, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN5404_c0_g1_i1", "attributes": {"ID": ["TRINITY_DN5404_c0_g1_i1|m.6938.utr5p1"], "Parent": ["TRINITY_DN5404_c0_g1_i1|m.6938"]}, "strand": "-"}, {"featuretype": "exon", "end": 344, "score": ".", "start": 1, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN5404_c0_g1_i1", "attributes": {"ID": ["TRINITY_DN5404_c0_g1_i1|m.6938.exon1"], "Parent": ["TRINITY_DN5404_c0_g1_i1|m.6938"]}, "strand": "-"}, {"featuretype": "CDS", "end": 342, "score": ".", "start": 1, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN5404_c0_g1_i1", "attributes": {"ID": ["cds.TRINITY_DN5404_c0_g1_i1|m.6938"], "Parent": ["TRINITY_DN5404_c0_g1_i1|m.6938"]}, "strand": "-"}, {"featuretype": "gene", "end": 605, "score": ".", "start": 1, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN5409_c0_g1_i1", "attributes": {"ID": ["TRINITY_DN5409_c0_g1_i1|g.6942"], "Name": ["ORF%20TRINITY_DN5409_c0_g1_i1%7Cg.6942%20TRINITY_DN5409_c0_g1_i1%7Cm.6942%20type%3Ainternal%20len%3A202%20%28-%29"]}, "strand": "-"}, {"featuretype": "mRNA", "end": 605, "score": ".", "start": 1, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN5409_c0_g1_i1", "attributes": {"ID": ["TRINITY_DN5409_c0_g1_i1|m.6942"], "Parent": ["TRINITY_DN5409_c0_g1_i1|g.6942"], "Name": ["ORF%20TRINITY_DN5409_c0_g1_i1%7Cg.6942%20TRINITY_DN5409_c0_g1_i1%7Cm.6942%20type%3Ainternal%20len%3A202%20%28-%29"]}, "strand": "-"}, {"featuretype": "five_prime_UTR", "end": 605, "score": ".", "start": 604, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN5409_c0_g1_i1", "attributes": {"ID": ["TRINITY_DN5409_c0_g1_i1|m.6942.utr5p1"], "Parent": ["TRINITY_DN5409_c0_g1_i1|m.6942"]}, "strand": "-"}, {"featuretype": "exon", "end": 605, "score": ".", "start": 1, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN5409_c0_g1_i1", "attributes": {"ID": ["TRINITY_DN5409_c0_g1_i1|m.6942.exon1"], "Parent": ["TRINITY_DN5409_c0_g1_i1|m.6942"]}, "strand": "-"}, {"featuretype": "CDS", "end": 603, "score": ".", "start": 1, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN5409_c0_g1_i1", "attributes": {"ID": ["cds.TRINITY_DN5409_c0_g1_i1|m.6942"], "Parent": ["TRINITY_DN5409_c0_g1_i1|m.6942"]}, "strand": "-"}, {"featuretype": "gene", "end": 1934, "score": ".", "start": 1, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN540_c0_g1_i1", "attributes": {"ID": ["TRINITY_DN540_c0_g1_i1|g.650"], "Name": ["ORF%20TRINITY_DN540_c0_g1_i1%7Cg.650%20TRINITY_DN540_c0_g1_i1%7Cm.650%20type%3Acomplete%20len%3A407%20%28%2B%29"]}, "strand": "+"}, {"featuretype": "mRNA", "end": 1934, "score": ".", "start": 1, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN540_c0_g1_i1", "attributes": {"ID": ["TRINITY_DN540_c0_g1_i1|m.650"], "Parent": ["TRINITY_DN540_c0_g1_i1|g.650"], "Name": ["ORF%20TRINITY_DN540_c0_g1_i1%7Cg.650%20TRINITY_DN540_c0_g1_i1%7Cm.650%20type%3Acomplete%20len%3A407%20%28%2B%29"]}, "strand": "+"}]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/js/editgff.js Sat Jun 24 14:55:25 2017 -0400 @@ -0,0 +1,68 @@ +var jsonobj=[] + $.ajax({url: "gff.json", success: function(result){ + jsonobj = result; + }}); + + +function merge_prediction() { + var lpart = document.getElementById("lpart").value; + var rpart = document.getElementById("rpart").value; + edit_annot(lpart,rpart); +} + + + + +function edit_annot(lpart,rpart) { + for (var i = jsonobj.length -1; i >= 0 ; i--) { + if (jsonobj[i].attributes.hasOwnProperty("Parent")) { + if (jsonobj[i].attributes.Parent[0] === lpart){ + if (jsonobj[i].featuretype == "three_prime_UTR") { + jsonobj.splice(i,1); + console.log("removed lpart three_prime_UTR"); + } + else { + jsonobj[i].attributes.Parent[0] = '.'.join(lpart,1); + } + } + if (jsonobj[i].attributes.Parent[0] === rpart){ + if (jsonobj[i].featuretype == "five_prime_UTR") { + jsonobj.splice(i,1); + console.log("removed rpart five_prime_UTR"); + } + else { + jsonobj[i].attributes.Parent[0] = '.'.join(lpart,1); + } + } + } + + }; +} + +function export_gff() { + var text=""; + var line=""; + for (var i=0;i<jsonobj.length;i++){ + var attributes=""; + for (var attribute in jsonobj[i].attributes){ + attributes=attribute+'='+jsonobj[i].attributes[attribute][0]+';'; + } + line = jsonobj[i].seqid+'\t'+ + jsonobj[i].source+'\t'+ + jsonobj[i].featuretype+'\t'+ + jsonobj[i].start+'\t'+ + jsonobj[i].end+'\t'+ + jsonobj[i].score+'\t'+ + jsonobj[i].strand+'\t'+ + jsonobj[i].frame+'\t'+ + attributes; + text=text+line+'\''; + } + var gfffile = new Blob([text], {type: "text/plain;charset=utf-8"}); + var blob = new Blob([text], {type: "text/plain;charset=utf-8"}); + var link = document.createElement('a'); + link.setAttribute('href', window.URL.createObjectURL(blob)); + link.setAttribute('download', "gff_export"); + link.click(); +} +
--- a/static/js/gff_app.js Sat Jun 17 15:10:53 2017 -0400 +++ b/static/js/gff_app.js Sat Jun 24 14:55:25 2017 -0400 @@ -17,20 +17,18 @@ //enableHorizontalScrollbar: 0, //enableVerticalScrollbar: 1, columnDefs: [ - { name: 'contig', grouping: { groupPriority: 0 }, sort: { priority: 0, direction: 'desc' }, width: '25%', cellTemplate: '<div><div ng-if="!col.grouping || col.grouping.groupPriority === undefined || col.grouping.groupPriority === null || ( row.groupHeader && col.grouping.groupPriority === row.treeLevel )" class="ui-grid-cell-contents" title="TOOLTIP">{{COL_FIELD CUSTOM_FILTERS}}</div></div>' }, + { name: 'Contig', grouping: { groupPriority: 0 }, sort: { priority: 0, direction: 'desc' }, width: '25%', cellTemplate: '<div><div ng-if="!col.grouping || col.grouping.groupPriority === undefined || col.grouping.groupPriority === null || ( row.groupHeader && col.grouping.groupPriority === row.treeLevel )" class="ui-grid-cell-contents" title="TOOLTIP">{{COL_FIELD CUSTOM_FILTERS}}</div></div>' }, { name: 'mRNA', grouping: { groupPriority: 1 }, sort: { priority: 1,direction: 'desc' }, width: '25%', cellTemplate: '<div><div ng-if="!col.grouping || col.grouping.groupPriority === undefined || col.grouping.groupPriority === null || ( row.groupHeader && col.grouping.groupPriority === row.treeLevel )" class="ui-grid-cell-contents" title="TOOLTIP">{{COL_FIELD CUSTOM_FILTERS}}</div></div>' }, - { name: 'prediction', width: '25%' }, - { name: 'source', width: '10%' }, - { name: 'score', width: '5%'}, + { name: 'Prediction', width: '25%' }, + { name: 'Source', width: '10%' }, + { name: 'Score', width: '5%'}, ], onRegisterApi: function( gridApi ) { $scope.gridApi = gridApi; } }; - //var baseurl= '/api/datasets/'+hdaId+'?provider=sqlite-dict&data_type=raw_data&query='; - //var select="select%20seqid,seqid,source,featuretype,start,end,score,strand,frame,attributes%20from%20features"; - //var url= baseurl + select; + $http.get('trans.json') .success (function(response){ $scope.gridOptions.data = response;
--- a/static/trinotateviz.html Sat Jun 17 15:10:53 2017 -0400 +++ b/static/trinotateviz.html Sat Jun 24 14:55:25 2017 -0400 @@ -8,9 +8,12 @@ <script src="http://ui-grid.info/docs/grunt-scripts/pdfmake.js"></script> <script src="http://ui-grid.info/docs/grunt-scripts/vfs_fonts.js"></script> <script src="https://cdn.rawgit.com/angular-ui/bower-ui-grid/master/ui-grid.min.js"></script> + <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.1.0/jquery.min.js"></script> + <script src="editgff.js"></script> + <link rel="stylesheet" href="https://cdn.rawgit.com/angular-ui/bower-ui-grid/master/ui-grid.min.css" type="text/css"> - <link rel="stylesheet" href="main.css" type="text/css"> - <link rel="stylesheet" type="text/css" href="css/genome.css"> + <link rel="stylesheet" href="main.css" type="text/css"> + <link rel="stylesheet" type="text/css" href="css/genome.css"> </head> <body> @@ -18,6 +21,12 @@ <div ui-grid="gridOptions" ui-grid-pagination ui-grid-grouping ui-grid-exporter class="grid"></div> </div> +<div><br> +left part: <input type="text" name="lpart" id="lpart"> +right part: <input type="text" name="rpart" id="rpart"> +<input type="button" value="Submit" onClick="merge_prediction() ></input> +<input type="button" value="export" onClick="export_gff() ></input> +<br></div> <div id="GenomeBrowser" style="height: 100%; width: 100%; padding: 0; border: 0;"></div> <div style="display: none">JBrowseDefaultMainPage</div> @@ -123,4 +132,5 @@ </script> <script src="gff_app.js"></script> </body> + </html>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gff.json Sat Jun 24 14:55:25 2017 -0400 @@ -0,0 +1,1 @@ +[{"featuretype": "gene", "end": 344, "score": ".", "start": 1, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN5404_c0_g1_i1", "attributes": {"ID": ["TRINITY_DN5404_c0_g1_i1|g.6938"], "Name": ["ORF%20TRINITY_DN5404_c0_g1_i1%7Cg.6938%20TRINITY_DN5404_c0_g1_i1%7Cm.6938%20type%3Ainternal%20len%3A115%20%28-%29"]}, "strand": "-"}, {"featuretype": "mRNA", "end": 344, "score": ".", "start": 1, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN5404_c0_g1_i1", "attributes": {"ID": ["TRINITY_DN5404_c0_g1_i1|m.6938"], "Parent": ["TRINITY_DN5404_c0_g1_i1|g.6938"], "Name": ["ORF%20TRINITY_DN5404_c0_g1_i1%7Cg.6938%20TRINITY_DN5404_c0_g1_i1%7Cm.6938%20type%3Ainternal%20len%3A115%20%28-%29"]}, "strand": "-"}, {"featuretype": "five_prime_UTR", "end": 344, "score": ".", "start": 343, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN5404_c0_g1_i1", "attributes": {"ID": ["TRINITY_DN5404_c0_g1_i1|m.6938.utr5p1"], "Parent": ["TRINITY_DN5404_c0_g1_i1|m.6938"]}, "strand": "-"}, {"featuretype": "exon", "end": 344, "score": ".", "start": 1, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN5404_c0_g1_i1", "attributes": {"ID": ["TRINITY_DN5404_c0_g1_i1|m.6938.exon1"], "Parent": ["TRINITY_DN5404_c0_g1_i1|m.6938"]}, "strand": "-"}, {"featuretype": "CDS", "end": 342, "score": ".", "start": 1, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN5404_c0_g1_i1", "attributes": {"ID": ["cds.TRINITY_DN5404_c0_g1_i1|m.6938"], "Parent": ["TRINITY_DN5404_c0_g1_i1|m.6938"]}, "strand": "-"}, {"featuretype": "gene", "end": 605, "score": ".", "start": 1, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN5409_c0_g1_i1", "attributes": {"ID": ["TRINITY_DN5409_c0_g1_i1|g.6942"], "Name": ["ORF%20TRINITY_DN5409_c0_g1_i1%7Cg.6942%20TRINITY_DN5409_c0_g1_i1%7Cm.6942%20type%3Ainternal%20len%3A202%20%28-%29"]}, "strand": "-"}, {"featuretype": "mRNA", "end": 605, "score": ".", "start": 1, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN5409_c0_g1_i1", "attributes": {"ID": ["TRINITY_DN5409_c0_g1_i1|m.6942"], "Parent": ["TRINITY_DN5409_c0_g1_i1|g.6942"], "Name": ["ORF%20TRINITY_DN5409_c0_g1_i1%7Cg.6942%20TRINITY_DN5409_c0_g1_i1%7Cm.6942%20type%3Ainternal%20len%3A202%20%28-%29"]}, "strand": "-"}, {"featuretype": "five_prime_UTR", "end": 605, "score": ".", "start": 604, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN5409_c0_g1_i1", "attributes": {"ID": ["TRINITY_DN5409_c0_g1_i1|m.6942.utr5p1"], "Parent": ["TRINITY_DN5409_c0_g1_i1|m.6942"]}, "strand": "-"}, {"featuretype": "exon", "end": 605, "score": ".", "start": 1, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN5409_c0_g1_i1", "attributes": {"ID": ["TRINITY_DN5409_c0_g1_i1|m.6942.exon1"], "Parent": ["TRINITY_DN5409_c0_g1_i1|m.6942"]}, "strand": "-"}, {"featuretype": "CDS", "end": 603, "score": ".", "start": 1, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN5409_c0_g1_i1", "attributes": {"ID": ["cds.TRINITY_DN5409_c0_g1_i1|m.6942"], "Parent": ["TRINITY_DN5409_c0_g1_i1|m.6942"]}, "strand": "-"}, {"featuretype": "gene", "end": 1934, "score": ".", "start": 1, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN540_c0_g1_i1", "attributes": {"ID": ["TRINITY_DN540_c0_g1_i1|g.650"], "Name": ["ORF%20TRINITY_DN540_c0_g1_i1%7Cg.650%20TRINITY_DN540_c0_g1_i1%7Cm.650%20type%3Acomplete%20len%3A407%20%28%2B%29"]}, "strand": "+"}, {"featuretype": "mRNA", "end": 1934, "score": ".", "start": 1, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN540_c0_g1_i1", "attributes": {"ID": ["TRINITY_DN540_c0_g1_i1|m.650"], "Parent": ["TRINITY_DN540_c0_g1_i1|g.650"], "Name": ["ORF%20TRINITY_DN540_c0_g1_i1%7Cg.650%20TRINITY_DN540_c0_g1_i1%7Cm.650%20type%3Acomplete%20len%3A407%20%28%2B%29"]}, "strand": "+"}, {"featuretype": "five_prime_UTR", "end": 349, "score": ".", "start": 1, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN540_c0_g1_i1", "attributes": {"ID": ["TRINITY_DN540_c0_g1_i1|m.650.utr5p1"], "Parent": ["TRINITY_DN540_c0_g1_i1|m.650"]}, "strand": "+"}, {"featuretype": "exon", "end": 1934, "score": ".", "start": 1, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN540_c0_g1_i1", "attributes": {"ID": ["TRINITY_DN540_c0_g1_i1|m.650.exon1"], "Parent": ["TRINITY_DN540_c0_g1_i1|m.650"]}, "strand": "+"}, {"featuretype": "CDS", "end": 1570, "score": ".", "start": 350, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN540_c0_g1_i1", "attributes": {"ID": ["cds.TRINITY_DN540_c0_g1_i1|m.650"], "Parent": ["TRINITY_DN540_c0_g1_i1|m.650"]}, "strand": "+"}, {"featuretype": "three_prime_UTR", "end": 1934, "score": ".", "start": 1571, "frame": ".", "source": "transdecoder", "seqid": "TRINITY_DN540_c0_g1_i1", "attributes": {"ID": ["TRINITY_DN540_c0_g1_i1|m.650.utr3p1"], "Parent": ["TRINITY_DN540_c0_g1_i1|m.650"]}, "strand": "+"}, {"featuretype": "gene", "end": 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