Refseq codon composition calculation

modules/analysis/refseq/calculateCompositionCodonA.js

@@ -0,0 +1,190 @@
+function calculateCompositionCodonA() {
+
+	// Script to calculate amino acid composition in reference sequences
+
+	var codingFeatures = {};
+	var resultMap = glue.command(["list", "feature","-w", "featureMetatags.name = 'CODES_AMINO_ACIDS'"]);
+	var featureList = resultMap["listResult"];
+	var codingFeatureList = featureList["row"];
+	_.each(codingFeatureList,function(featureObj){
+
+		//glue.log("INFO", "RESULT WAS ", featureObj);
+
+		var valueArray = featureObj["value"];
+		var codingFeatureName = valueArray[0];
+		//glue.log("INFO", "NAME WAS ", featureName)
+		codingFeatures[codingFeatureName] = featureObj;
+
+
+	});	
+	//glue.log("INFO", "RESULT WAS ", codingFeatures);
+
+	// get list of reference sequences from GLUE
+	var referencesResult = glue.command(["list","reference"]);
+	//glue.log("INFO", "RESULT WAS ", referencesResult);
+
+	var listResult = referencesResult["listResult"];
+	var referencesList = listResult["row"];
+	//glue.log("INFO", "RESULT WAS ", referencesList);
+
+
+	// iterate through reference list and get AA composition of each coding feature
+	codonCompositionResults = {}
+	_.each(referencesList, function(refObj) {
+
+		//glue.log("INFO", "RESULT WAS ", refObj);
+
+		var refseqResults = {};
+		var referenceProperties = refObj["value"];
+		var referenceName = referenceProperties[0];
+
+		//glue.log("INFO", "Reference name result was:", referenceName);
+
+		// list all features annotated in this reference 
+		// GLUE COMMAND: reference [referenceName] list feature-location
+		glue.inMode("/reference/"+referenceName, function() {
+
+			var featuresResult = glue.tableToObjects(glue.command(["list", "feature-location"]));
+			//glue.log("INFO", "RESULT WAS ", featuresResult);
+
+			// iterate through features
+			_.each(featuresResult, function(featureObj) {
+
+			   //glue.log("INFO", "RESULT WAS ", featureObj);
+
+			   var featureResults = {};
+
+			   // get amino acid sequence
+			   var featureName = featureObj["feature.name"];
+			   //glue.log("INFO", "Feature name result was:", featureName);
+
+			   // get amino acid sequence of the features
+			   if (codingFeatures[featureName]) {
+
+				   glue.inMode("/feature-location/"+featureName, function() {
+
+					   var codonSequenceResult = glue.tableToObjects(glue.command(["amino-acid"]));
+
+					   //glue.log("INFO", "Table result was:", codonSequenceResult);
+
+					   // iterate through and get codon composition of feature
+					   var length = 0;
+					   _.each(codonSequenceResult, function(codonObj) {
+
+						   var codon = codonObj["codonNts"];
+
+						   length += 1;
+
+						   //glue.log("INFO", "Amino acid residue result was:", codon);
+
+						   if (featureResults[codon]) {
+
+							   featureResults[codon] += 1;
+
+						   }
+						   else {
+
+							   featureResults[codon] = 1;
+						   }
+
+					   });
+
+					   featureResults["length"] = length;
+
+				   });
+
+				  // store feature result
+				  refseqResults[featureName] = featureResults;
+
+				}
+
+			});   
+
+			// store reference result
+			codonCompositionResults[referenceName] = refseqResults;
+
+		});   
+
+	});
+
+	//glue.log("INFO", "FINAL RESULT WAS ", codonCompositionResults);
+
+	// Transform the data 
+	var outputArray = [];
+    var headerRowCodons = [ 'ATT', 'ATC', 'ATA', 'ATG', 'ACT', 'ACC', 'ACA', 'ACG',
+                            'AGT', 'AGC', 'AGA', 'AGG', 'AAT', 'AAC', 'AAA', 'AAG'  ];
+
+	// Iterate through reference sequences
+	_.each(_.keys(codonCompositionResults), function(referenceName) {
+
+		glue.log("INFO", "Got reference name '"+referenceName);
+
+		// Iterate through reference sequence features
+		var featuresObj = codonCompositionResults[referenceName];
+
+		_.each(_.keys(featuresObj), function(featureName) {
+
+		   // Write values for each amino (count + ratio) 
+		   var codonObj = featuresObj[featureName];
+		   var length = codonObj["length"];
+		   //glue.log("INFO", "Got reference name '"+referenceName+" and feature "+featureName+" length = "+length);
+
+
+		   var codonCountResults = {};
+		   var codonFreqResults = {};
+		   _.each(headerRowCodons, function(codon) {
+
+			   var codonFreq;
+			   var codonCount = codonObj[codon];
+			   if (codonCount) {
+					var codonFreq = (codonCount / length) * 100;
+					var codonFormatedFreq = codonFreq.toFixed(2);
+					//glue.log("INFO", "  Amino acid '"+codon+" frequency = ("+codonCount+" / "+length+") "+codonFormatedFreq);
+			   }
+			   else {
+				    codonCount = '0';
+				    codonFormatedFreq = '0';		  
+			   }
+
+			  codonCountResults[codon] = codonCount;
+			  codonFreqResults[codon] = codonFormatedFreq;
+
+		   });
+
+		   // add results to array to be returned to GLUE
+		   outputArray.push({
+
+
+			   referenceName: referenceName,
+			   featureName: featureName,
+			   seqLength: length,
+			   "ATT%": codonFreqResults["ATT"],
+			   "ATC%": codonFreqResults["ATC"],
+			   "ATA%": codonFreqResults["ATA"],
+			   "ATG%": codonFreqResults["ATG"],
+			   "AGA%": codonFreqResults["AGA"],		   
+			   "AGG%": codonFreqResults["AGG"],
+			   "AGT%": codonFreqResults["AGT"],
+			   "AGC%": codonFreqResults["AGC"],
+			   "ACT%": codonFreqResults["ACT"],
+			   "ACC%": codonFreqResults["ACC"],
+			   "AAG%": codonFreqResults["AAG"],
+			   "ACA%": codonFreqResults["ACA"],
+			   "ACG%": codonFreqResults["ACG"],
+			   "AAT%": codonFreqResults["AAT"],
+			   "AAC%": codonFreqResults["AAC"],
+			   "AAA%": codonFreqResults["AAA"],
+			   "AAG%": codonFreqResults["AAG"]
+
+		   });
+
+
+		});
+
+
+	});
+
+	return outputArray;
+}
+
+

modules/analysis/refseq/calculateCompositionCodonA.xml

@@ -0,0 +1,13 @@
+<ecmaFunctionInvoker>
+
+	<scriptFileName>calculateCompositionCodonA.js</scriptFileName>
+
+	<function>
+		<name>calculateCompositionCodonA</name>
+
+		<tableFromObjectsResultType/>
+	</function>
+
+</ecmaFunctionInvoker>
+
+

modules/analysis/refseq/calculateCompositionCodonC.js

@@ -0,0 +1,193 @@
+function calculateCompositionCodonC() {
+
+	// Script to calculate amino acid composition in reference sequences
+
+	var codingFeatures = {};
+	var resultMap = glue.command(["list", "feature","-w", "featureMetatags.name = 'CODES_AMINO_ACIDS'"]);
+	var featureList = resultMap["listResult"];
+	var codingFeatureList = featureList["row"];
+	_.each(codingFeatureList,function(featureObj){
+
+		//glue.log("INFO", "RESULT WAS ", featureObj);
+
+		var valueArray = featureObj["value"];
+		var codingFeatureName = valueArray[0];
+		//glue.log("INFO", "NAME WAS ", featureName)
+		codingFeatures[codingFeatureName] = featureObj;
+
+
+	});	
+	//glue.log("INFO", "RESULT WAS ", codingFeatures);
+
+	// get list of reference sequences from GLUE
+	var referencesResult = glue.command(["list","reference"]);
+	//glue.log("INFO", "RESULT WAS ", referencesResult);
+
+	var listResult = referencesResult["listResult"];
+	var referencesList = listResult["row"];
+	//glue.log("INFO", "RESULT WAS ", referencesList);
+
+
+	// iterate through reference list and get AA composition of each coding feature
+	codonCompositionResults = {}
+	_.each(referencesList, function(refObj) {
+
+		//glue.log("INFO", "RESULT WAS ", refObj);
+
+		var refseqResults = {};
+		var referenceProperties = refObj["value"];
+		var referenceName = referenceProperties[0];
+
+		//glue.log("INFO", "Reference name result was:", referenceName);
+
+		// list all features annotated in this reference 
+		// GLUE COMMAND: reference [referenceName] list feature-location
+		glue.inMode("/reference/"+referenceName, function() {
+
+			var featuresResult = glue.tableToObjects(glue.command(["list", "feature-location"]));
+			//glue.log("INFO", "RESULT WAS ", featuresResult);
+
+			// iterate through features
+			_.each(featuresResult, function(featureObj) {
+
+			   //glue.log("INFO", "RESULT WAS ", featureObj);
+
+			   var featureResults = {};
+
+			   // get amino acid sequence
+			   var featureName = featureObj["feature.name"];
+			   //glue.log("INFO", "Feature name result was:", featureName);
+
+			   // get amino acid sequence of the features
+			   if (codingFeatures[featureName]) {
+
+				   glue.inMode("/feature-location/"+featureName, function() {
+
+					   var codonSequenceResult = glue.tableToObjects(glue.command(["amino-acid"]));
+
+					   //glue.log("INFO", "Table result was:", codonSequenceResult);
+
+					   // iterate through and get codon composition of feature
+					   var length = 0;
+					   _.each(codonSequenceResult, function(codonObj) {
+
+						   var codon = codonObj["codonNts"];
+
+						   length += 1;
+
+						   //glue.log("INFO", "Amino acid residue result was:", codon);
+
+						   if (featureResults[codon]) {
+
+							   featureResults[codon] += 1;
+
+						   }
+						   else {
+
+							   featureResults[codon] = 1;
+						   }
+
+					   });
+
+					   featureResults["length"] = length;
+
+				   });
+
+				  // store feature result
+				  refseqResults[featureName] = featureResults;
+
+				}
+
+			});   
+
+			// store reference result
+			codonCompositionResults[referenceName] = refseqResults;
+
+		});   
+
+	});
+
+	//glue.log("INFO", "FINAL RESULT WAS ", codonCompositionResults);
+
+	// Transform the data 
+	var outputArray = [];
+    var headerRowCodons = ['CTT', 'CTC', 'CTA', 'CTG', 'CCT', 'CCC', 'CCA', 'CCG',
+                           'CAG', 'CAT', 'CAC', 'CAA', 'CGT', 'CGC', 'CGA', 'CGG'  ];
+
+	// Iterate through reference sequences
+	_.each(_.keys(codonCompositionResults), function(referenceName) {
+
+		glue.log("INFO", "Got reference name '"+referenceName);
+
+		// Iterate through reference sequence features
+		var featuresObj = codonCompositionResults[referenceName];
+
+		_.each(_.keys(featuresObj), function(featureName) {
+
+		   // Write values for each amino (count + ratio) 
+		   var codonObj = featuresObj[featureName];
+		   var length = codonObj["length"];
+		   //glue.log("INFO", "Got reference name '"+referenceName+" and feature "+featureName+" length = "+length);
+
+
+		   var codonCountResults = {};
+		   var codonFreqResults = {};
+		   _.each(headerRowCodons, function(codon) {
+
+			   var codonFreq;
+			   var codonCount = codonObj[codon];
+			   if (codonCount) {
+					var codonFreq = (codonCount / length) * 100;
+					var codonFormatedFreq = codonFreq.toFixed(2);
+					//glue.log("INFO", "  Amino acid '"+codon+" frequency = ("+codonCount+" / "+length+") "+codonFormatedFreq);
+			   }
+			   else {
+				    codonCount = '0';
+				    codonFormatedFreq = '0';		  
+			   }
+
+			  codonCountResults[codon] = codonCount;
+			  codonFreqResults[codon] = codonFormatedFreq;
+
+		   });
+
+		   // add results to array to be returned to GLUE
+		   outputArray.push({
+
+
+			   referenceName: referenceName,
+			   featureName: featureName,
+			   seqLength: length,
+
+			   "CTT%": codonFreqResults["CTT"],
+			   "CTC%": codonFreqResults["CTC"],
+			   "CTA%": codonFreqResults["CTA"],
+			   "CTG%": codonFreqResults["CTG"],
+
+			   "CCT%": codonFreqResults["CCT"],
+			   "CCC%": codonFreqResults["CCC"],			   
+			   "CCA%": codonFreqResults["CCA"],
+			   "CCG%": codonFreqResults["CCG"],
+
+			   "CAA%": codonFreqResults["CAA"],		   
+			   "CAG%": codonFreqResults["CAG"],
+			   "CAT%": codonFreqResults["CAT"],		   
+			   "CAC%": codonFreqResults["CAC"],
+
+			   "CGT%": codonFreqResults["CGT"],		   
+			   "CGC%": codonFreqResults["CGC"],
+			   "CGA%": codonFreqResults["CGA"],
+			   "CGG%": codonFreqResults["CGG"],
+
+		   });
+
+
+		});
+
+
+	});
+
+	return outputArray;
+}
+
+