Merge branch 'master' of https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline

SCRIPTS/make_html.py

@@ -255,11 +255,11 @@ for c in conditionVS:
 			table['geneID'] = newGeneID
 
 			# We add some columns
+			precision = 5
 			table = table.assign(GenesInQuery = [int(q[1]) for q in table['GeneRatio'].str.split("/")])
 			table = table.assign(GenesInTermBackground = [int(q[0]) for q in table['BgRatio'].str.split("/")])
-			table = table.assign(GenesInOntologyBackground = [int(q[1]) for q in table['BgRatio'].str.split("/")])
-			table = table.assign(GeneQueryRatio = table['Count']/table['GenesInQuery'])
-			table = table.assign(GeneTermRatio = table['Count']/table['GenesInTermBackground'])
+			table = table.assign(GeneQueryRatio = round(table['Count']/table['GenesInQuery'], precision))
+			table = table.assign(GeneTermRatio = round(table['Count']/table['GenesInTermBackground'], precision))
 			# Format in scientific notation until we found a way in DataTable
 			table['pvalue'] = [str("%.2e" % s) for s in table['pvalue']]
 			table['p.adjust'] = [str("%.2e" % s) for s in table['p.adjust']]
@@ -269,9 +269,9 @@ for c in conditionVS:
 			table = table.rename(columns={'GeneRatio': 'GeneQueryRatio', 'pvalue' : 'pval', 'p.adjust' : 'padj', 'qvalue':'qval'})
 			# We select and order interesting columns
 			if annot == "annotGo":
-				table = table[['ONTOLOGY', 'ID', 'GeneTermRatio', 'GeneQueryRatio', 'pval', 'padj', 'qval', 'Description', 'Count', 'GenesInQuery', 'GenesInTermBackground', 'GenesInOntologyBackground', 'geneID']]
+				table = table[['ONTOLOGY', 'ID', 'GeneTermRatio', 'GeneQueryRatio', 'pval', 'padj', 'qval', 'Description', 'Count', 'GenesInQuery', 'GenesInTermBackground', 'geneID']]
 			else:
-				table = table[['ID', 'GeneTermRatio', 'GeneQueryRatio', 'pval', 'padj', 'qval', 'Description', 'Count', 'GenesInQuery', 'GenesInTermBackground', 'GenesInOntologyBackground', 'geneID']]
+				table = table[['ID', 'GeneTermRatio', 'GeneQueryRatio', 'pval', 'padj', 'qval', 'Description', 'Count', 'GenesInQuery', 'GenesInTermBackground', 'geneID']]
 			# We export them
 			templateVars["deseqres"][c["condition1"]+"__vs__"+c["condition2"]][annot] = dataframe_to_list_of_dicts(table)
 
@@ -328,7 +328,6 @@ for c in conditionVS:
 			g["number_of_genes_in_background"] = ls[3]
 			g["gene_ratio"] = str("%.2f" % (int(ls[2]) / int(ls[3])))
 			g["ncbiTaxonId"] = ls[4]
-			g["inputGenes"] = ', '.join(ls[5].split(','))
 			gc = []
 			for g1, g2 in zip(ls[5].split(','), ls[6].split(',')):
 				fc = templateVars["deseqres"][c["condition1"]+"__vs__"+c["condition2"]]["fc"][g1]
@@ -343,7 +342,6 @@ for c in conditionVS:
 					sign = ""
 				gc.append('<font color="{}">{}</font>'.format(color, g2))
 			g["coloredPreferredNames"] = ', '.join(gc)
-			g["preferredNames"] = ', '.join(ls[6].split(','))
 			g["p_value"] = ls[7]
 			g["fdr"] = ls[8]
 			g["description"] = ls[9]

TEMPLATE/index_SA.html

@@ -323,7 +323,6 @@
 													<th>Description</th>
 													<th>GenesInQuery</th>
 													<th>GenesInTermBackground</th>
-													<th>GenesInOntologyBackground"</th>
 													<th>geneID</th>
 												</tr>
 											</thead>
@@ -360,7 +359,6 @@
 													<th>Description</th>
 													<th>GenesInQuery</th>
 													<th>GenesInTermBackground</th>
-													<th>GenesInOntologyBackground"</th>
 													<th>geneID</th>
 												</tr>
 											</thead>
@@ -436,8 +434,6 @@
 												<th>Term</th>
 												<th>Count</th>
 												<th>Ratio&nbsp;of genes&nbsp;in&nbsp;term</th>
-												<th>inputGenes</th>
-												<th>preferredNames</th>
 												<th>pvalue</th>
 												<th>fdr</th>
 												<th>Description</th>
@@ -630,7 +626,7 @@
 
 	function gen_stringdb_table(table_id, comp){
 		var table = $('#'+table_id).DataTable({
-			"order": [[ 8, "asc" ]],
+			"order": [[ 6, "asc" ]],
 			"data":{{stringParams}}[comp]["enrich"],
 			"columns":[
 				{
@@ -643,18 +639,10 @@
 				{"data":"term"},
 				{"data":"number_of_genes"},
 				{"data":"gene_ratio"},
-				{"data":"inputGenes"},
-				{"data":"preferredNames"},
 				{"data":"p_value"},
 				{"data":"fdr"},
 				{"data":"description"}
 			],
-			"columnDefs": [
-				{
-					"targets": [ 5, 6 ],
-					"visible": false
-				}
-			],
 			"initComplete": function () {
 				this.api().columns([1]).every( function () {
 					var column = this;
@@ -733,12 +721,11 @@
 				{"data":"Description"},
 				{"data":"GenesInQuery", render: $.fn.dataTable.render.number( ' ', '.', 2)},
 				{"data":"GenesInTermBackground", render: $.fn.dataTable.render.number( ' ', '.', 2)},
-				{"data":"GenesInOntologyBackground", render: $.fn.dataTable.render.number( ' ', '.', 2)},
 				{"data":"geneID"}
 			],
 			"columnDefs": [
 				{
-					"targets": [ 10, 11, 12, 13 ],
+					"targets": [ 10, 11, 12 ],
 					"visible": false
 				}
 			],
@@ -801,12 +788,11 @@
 				{"data":"Description"},
 				{"data":"GenesInQuery", render: $.fn.dataTable.render.number( ' ', '.', 2)},
 				{"data":"GenesInTermBackground", render: $.fn.dataTable.render.number( ' ', '.', 2)},
-				{"data":"GenesInOntologyBackground", render: $.fn.dataTable.render.number( ' ', '.', 2)},
 				{"data":"geneID"}
 			],
 			"columnDefs": [
 				{
-					"targets": [ 9, 10, 11, 12 ],
+					"targets": [ 9, 10, 11 ],
 					"visible": false
 				}
 			]});