Added codon bias scripts.

modules/analysis/refseq/calculateCodonBias.js

@@ -0,0 +1,352 @@
+function calculateCodonBias() {
+
+	// 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];
+	    var sequenceID = referenceProperties[2];
+
+		//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 = {};
+			   var aaCounts = {};
+
+			   // 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"];
+					       var aa    = codonObj["aminoAcid"]; 
+
+					       // increment amino acid counts
+					       if (aaCounts[aa]) {
+
+					           aaCounts[aa] += 1;
+
+					       } else {
+					           aaCounts[aa] = 1;
+					       }
+
+						   length += 1;
+
+						   //glue.log("INFO", "Amino acid result:", aa);
+						   //glue.log("INFO", " Codon result:", codon);
+
+						   if (featureResults[aa]) {
+
+                               // get the map with codon counts for this aa
+                               aaCodonMap = featureResults[aa];							   
+							   aaCodonMap[codon] += 1;
+
+						   }
+						   else {
+
+					           // create a map with all codons for this aa as keys
+						       aaCodonMap = create_codon_map(aa);
+						       // increment the map for the current codon
+
+						       aaCodonMap[codon] = 1;
+
+						       // associate this data structure with the genome feature map
+						       // by using the current aa as a key
+						       featureResults[aa] = aaCodonMap;
+
+						   }
+
+					   });
+
+				       // store the counts for each amino acid
+				       featureResults["aa_counts"] = aaCounts;
+
+				       // store the total sequence length
+					   featureResults["length"] = length;
+
+					   // Store the feature name
+					   featureResults["feature_name"] = featureName;
+
+				   });
+
+                  //glue.log("INFO", "FEATURE RESULT WAS ", featureResults); die;
+
+				  // store feature result
+				  refseqResults[featureName] = featureResults;
+				  refseqResults["reference_name"] = referenceName;
+				  refseqResults["sequence_id"] = sequenceID;
+
+				}
+
+			});   
+
+			// store reference result
+			codonCompositionResults[referenceName] = refseqResults;
+
+		});   
+
+	});
+
+	// glue.log("INFO", "FINAL RESULT WAS ", codonCompositionResults);
+	var outputArray = [];
+
+	// get each reference
+
+	_.each(codonCompositionResults, function(refseqResults) {
+
+		//glue.log("INFO", "RESULT WAS ", refseqResults);
+
+		var referenceName = refseqResults["reference_name"];
+		var sequenceID = refseqResults["sequence_id"];
+
+		// get each feature
+	    _.each(refseqResults, function(featureResults) {
+
+			var featureName = featureResults["feature_name"];
+
+			// get each amino
+			aaCounts = featureResults["aa_counts"];
+		    var referenceName = refseqResults["reference_name"];			
+			_.each(_.keys(aaCounts), function(aa) {
+
+				var aaCount = aaCounts[aa];						
+				// glue.log("INFO", "Got count '"+count+"' for aa character'"+aa+"'");
+
+				var codonCounts = featureResults[aa];
+		    	//glue.log("INFO", "RESULT WAS ", codonCounts); die;		    	
+				_.each(_.keys(codonCounts), function(codon) {
+
+					var codonCount = codonCounts[codon];						
+
+	                // write line: reference - feature - aa - aa count - codon - codon count					
+					outputArray.push({
+
+						referenceName: referenceName,
+						sequenceID: sequenceID,
+						featureName: featureName,
+						aa: aa,
+						aaCount: aaCount,
+						codon: codon,
+						codonCount: codonCount
+
+					});
+
+
+				});
+
+			});
+
+	    });
+
+	});
+
+	return outputArray;
+}
+
+
+function create_codon_map(aa){
+
+	var codonMap = {};
+
+	if (aa == 'A') {
+
+		codonMap['GCT'] = 0;
+		codonMap['GCC'] = 0;
+		codonMap['GCA'] = 0;
+		codonMap['GCG'] = 0;
+
+	} else if (aa == 'C') {
+
+		codonMap['TGT'] = 0;
+		codonMap['TGC'] = 0;
+
+
+	} else if (aa == 'D') {
+
+		codonMap['GAT'] = 0;
+		codonMap['GAC'] = 0;
+
+	} else if (aa == 'E') {
+
+		codonMap['GAA'] = 0;
+		codonMap['GAG'] = 0;
+
+	} else if (aa == 'F') {
+
+		codonMap['TTT'] = 0;
+		codonMap['TTC'] = 0;
+
+	} else if (aa == 'G') {
+
+		codonMap['GGT'] = 0;
+		codonMap['GGC'] = 0;
+		codonMap['GGA'] = 0;
+		codonMap['GGG'] = 0;
+
+	} else if (aa == 'H') {
+
+		codonMap['CAT'] = 0;
+		codonMap['CAC'] = 0;
+
+	} else if (aa == 'I') {
+
+		codonMap['ATT'] = 0;
+		codonMap['ATC'] = 0;
+		codonMap['ATA'] = 0;
+
+	} else if (aa == 'K') {
+
+		codonMap['AAA'] = 0;
+		codonMap['AAG'] = 0;
+
+	} else if (aa == 'L') {
+
+		codonMap['CTT'] = 0;
+		codonMap['CTC'] = 0;
+		codonMap['CTA'] = 0;
+		codonMap['CTG'] = 0;
+		codonMap['TTA'] = 0;
+		codonMap['TTG'] = 0;
+
+
+	} else if (aa == 'M') {
+
+		codonMap['ATG'] = 0;
+
+	} else if (aa == 'N') {
+
+		codonMap['AAT'] = 0;
+		codonMap['AAC'] = 0;
+
+	} else if (aa == 'P') {
+
+		codonMap['CCT'] = 0;
+		codonMap['CCC'] = 0;
+		codonMap['CCA'] = 0;
+		codonMap['CCG'] = 0;
+
+	} else if (aa == 'Q') {
+
+		codonMap['CAA'] = 0;
+		codonMap['CAG'] = 0;
+
+	} else if (aa == 'R') {
+
+		codonMap['CGT'] = 0;
+		codonMap['CGC'] = 0;
+		codonMap['CGA'] = 0;
+		codonMap['CGG'] = 0;
+		codonMap['AGA'] = 0;
+		codonMap['AGG'] = 0;
+
+	} else if (aa == 'S') {
+
+		codonMap['TCT'] = 0;
+		codonMap['TCC'] = 0;
+		codonMap['TCA'] = 0;
+		codonMap['TCG'] = 0;
+		codonMap['AGT'] = 0;
+		codonMap['AGC'] = 0;
+
+	} else if (aa == 'T') {
+
+		codonMap['ACT'] = 0;
+		codonMap['ACC'] = 0;
+		codonMap['ACA'] = 0;
+		codonMap['ACG'] = 0;
+
+	} else if (aa == 'V') {
+
+		codonMap['GTT'] = 0;
+		codonMap['GTC'] = 0;
+		codonMap['GTA'] = 0;
+		codonMap['GTG'] = 0;
+
+	} else if (aa == 'W') {
+
+		codonMap['TGG'] = 0;
+
+	} else if (aa == 'Y') {
+
+		codonMap['TAT'] = 0;
+		codonMap['TAC'] = 0;
+
+	} else if (aa == '*') {
+
+		codonMap['TAA'] = 0;
+		codonMap['TAG'] = 0;
+		codonMap['TGA'] = 0;
+
+	} else if (aa == 'X') {
+
+		codonMap['NNN'] = 0;
+
+	} else {
+
+		glue.log("INFO", "AMINO RESULT WAS ", aa);
+		die;	
+
+
+	} 
+
+    return codonMap;
+
+}
+
+
+

modules/analysis/refseq/calculateCodonBias.xml

@@ -0,0 +1,12 @@
+<ecmaFunctionInvoker>
+
+	<scriptFileName>calculateCodonBias.js</scriptFileName>
+
+	<function>
+		<name>calculateCodonBias</name>
+
+		<tableFromObjectsResultType/>
+	</function>
+
+</ecmaFunctionInvoker> 
+