/***************************************************** Amino Acid Preference Toolkit in Java Pathogen Project Department of Computer Science and Engineering University of South Carolina Columbia, SC 29208 Contact Email: rose@cse.sc.edu *****************************************************/ import java.io.*; import java.util.*; public class TriplePreferenceMultiSegment { public static void main(String[] args) { //args[0] = fasta filename //args[1] = gene filename //args[2] = output filename try { TriplePreferenceMultiSegment ntpms = new TriplePreferenceMultiSegment(args[0], args[1], args[2]); } catch (Exception exception) { exception.printStackTrace(); } } public TriplePreferenceMultiSegment(String fastaFileName, String geneFileName, String outputFileName) throws Exception { Hashtable codonToAminoAcidMap = new Hashtable(); codonToAminoAcidMap.put("CGA", "R"); codonToAminoAcidMap.put("CGC", "R"); codonToAminoAcidMap.put("CGG", "R"); codonToAminoAcidMap.put("CGT", "R"); codonToAminoAcidMap.put("AGA", "R"); codonToAminoAcidMap.put("AGG", "R"); codonToAminoAcidMap.put("CTA", "L"); codonToAminoAcidMap.put("CTC", "L"); codonToAminoAcidMap.put("CTG", "L"); codonToAminoAcidMap.put("CTT", "L"); codonToAminoAcidMap.put("TTA", "L"); codonToAminoAcidMap.put("TTG", "L"); codonToAminoAcidMap.put("TCA", "S"); codonToAminoAcidMap.put("TCC", "S"); codonToAminoAcidMap.put("TCG", "S"); codonToAminoAcidMap.put("TCT", "S"); codonToAminoAcidMap.put("AGC", "S"); codonToAminoAcidMap.put("AGT", "S"); codonToAminoAcidMap.put("ACA", "T"); codonToAminoAcidMap.put("ACC", "T"); codonToAminoAcidMap.put("ACG", "T"); codonToAminoAcidMap.put("ACT", "T"); codonToAminoAcidMap.put("CCA", "P"); codonToAminoAcidMap.put("CCC", "P"); codonToAminoAcidMap.put("CCG", "P"); codonToAminoAcidMap.put("CCT", "P"); codonToAminoAcidMap.put("GCA", "A"); codonToAminoAcidMap.put("GCC", "A"); codonToAminoAcidMap.put("GCG", "A"); codonToAminoAcidMap.put("GCT", "A"); codonToAminoAcidMap.put("GGA", "G"); codonToAminoAcidMap.put("GGC", "G"); codonToAminoAcidMap.put("GGG", "G"); codonToAminoAcidMap.put("GGT", "G"); codonToAminoAcidMap.put("GTA", "V"); codonToAminoAcidMap.put("GTC", "V"); codonToAminoAcidMap.put("GTG", "V"); codonToAminoAcidMap.put("GTT", "V"); codonToAminoAcidMap.put("AAA", "K"); codonToAminoAcidMap.put("AAG", "K"); codonToAminoAcidMap.put("AAC", "N"); codonToAminoAcidMap.put("AAT", "N"); codonToAminoAcidMap.put("CAA", "Q"); codonToAminoAcidMap.put("CAG", "Q"); codonToAminoAcidMap.put("CAC", "H"); codonToAminoAcidMap.put("CAT", "H"); codonToAminoAcidMap.put("GAA", "E"); codonToAminoAcidMap.put("GAG", "E"); codonToAminoAcidMap.put("GAC", "D"); codonToAminoAcidMap.put("GAT", "D"); codonToAminoAcidMap.put("TAC", "Y"); codonToAminoAcidMap.put("TAT", "Y"); codonToAminoAcidMap.put("TGC", "C"); codonToAminoAcidMap.put("TGT", "C"); codonToAminoAcidMap.put("TTC", "F"); codonToAminoAcidMap.put("TTT", "F"); codonToAminoAcidMap.put("ATA", "I"); codonToAminoAcidMap.put("ATC", "I"); codonToAminoAcidMap.put("ATT", "I"); codonToAminoAcidMap.put("ATG", "M"); codonToAminoAcidMap.put("TGG", "W"); codonToAminoAcidMap.put("TAA", "Z"); codonToAminoAcidMap.put("TAG", "Z"); codonToAminoAcidMap.put("TGA", "Z"); Hashtable aminoToIndexMap = new Hashtable(); aminoToIndexMap.put("A", new Integer(0)); aminoToIndexMap.put("C", new Integer(1)); aminoToIndexMap.put("D", new Integer(2)); aminoToIndexMap.put("E", new Integer(3)); aminoToIndexMap.put("F", new Integer(4)); aminoToIndexMap.put("G", new Integer(5)); aminoToIndexMap.put("H", new Integer(6)); aminoToIndexMap.put("I", new Integer(7)); aminoToIndexMap.put("K", new Integer(8)); aminoToIndexMap.put("L", new Integer(9)); aminoToIndexMap.put("M", new Integer(10)); aminoToIndexMap.put("N", new Integer(11)); aminoToIndexMap.put("P", new Integer(12)); aminoToIndexMap.put("Q", new Integer(13)); aminoToIndexMap.put("R", new Integer(14)); aminoToIndexMap.put("S", new Integer(15)); aminoToIndexMap.put("T", new Integer(16)); aminoToIndexMap.put("V", new Integer(17)); aminoToIndexMap.put("W", new Integer(18)); aminoToIndexMap.put("Y", new Integer(19)); aminoToIndexMap.put("Z", new Integer(20)); SequenceReader sequenceReader = new SequenceReader(); SequenceUtilities sequenceUtilities = new SequenceUtilities(); double[] triplePreferenceArray = new double[8000]; for (int i = 0; i < 8000; i++) { triplePreferenceArray[i] = 0; } double sum = 0; AminoAcidTriplePreference aminoAcidTriplePreference = new AminoAcidTriplePreference(); // go through genes, make full genes when necessary, call // triple preference function to generate individual gene preference // sum for total // since this if for multi-segmented genomes, go through all segments System.out.println("Reading multisegment file: " + fastaFileName); BufferedReader segmentFastaReader = new BufferedReader(new FileReader(fastaFileName)); BufferedReader segmentGeneReader = new BufferedReader(new FileReader(geneFileName)); String fastaLine, geneLine; while ((fastaLine = segmentFastaReader.readLine()) != null) { geneLine = segmentGeneReader.readLine(); System.out.println("Working on segment: Fasta File => " + fastaLine + " Gene File => " + geneLine); char[] sequence = sequenceReader.parseFastaFile(fastaLine).toCharArray(); char[] complementSequence = sequenceUtilities.complementSequence(sequence); int sequenceLength = sequence.length; ExtractGenes extractGenesObject = new ExtractGenes(geneLine); int[][] geneIndex = extractGenesObject.getGeneArray(); int numberOfGenes = extractGenesObject.getNumberOfGenes(); int geneCount = 0; StringBuffer currentCodonSequenceBuffer = new StringBuffer(); while (geneCount < numberOfGenes) { int geneStart = geneIndex[geneCount][0]; int geneStop = geneIndex[geneCount][1]; int geneStrand = geneIndex[geneCount][2]; int geneContinues = geneIndex[geneCount][3]; //System.out.println("Start: " + geneStart + " Stop: " + geneStop + " Strand: " + geneStrand + " Continues: " + geneContinues); int geneLength = (geneStop - geneStart + 1); if (geneStrand == 0) { if (geneStart > 0) { for (int i = (geneStart - 1); i < geneStop; i++) { currentCodonSequenceBuffer.append(sequence[i]); } } else { for (int i = sequenceLength + geneStart; i < sequenceLength; i++) //the part of the gene that is at the end of the genome { currentCodonSequenceBuffer.append(sequence[i]); } for (int i = 0; i < geneStop; i++) // the part of the gene that is at the beginning of the genome { currentCodonSequenceBuffer.append(sequence[i]); } } } else // complement strand { if (geneStart > 0) { // take from reverse complement StringBuffer newSequenceBuffer = new StringBuffer(); for (int i = (geneStop -1); i >= (geneStart - 1); i--) { // stick the new code in the front if in continues newSequenceBuffer.append(complementSequence[i]); } if (currentCodonSequenceBuffer.length() > 0) // continues currentCodonSequenceBuffer.insert(0,newSequenceBuffer.toString()); else currentCodonSequenceBuffer = newSequenceBuffer; } else { System.out.println("This case should never occur!"); } } if (geneContinues == 1) // we are not continuing, so compute aminos { char[] codonSequence = currentCodonSequenceBuffer.toString().toCharArray(); //System.out.println("Current codon sequence: " + new String(codonSequence)); char[] aminoAcidSequence = sequenceUtilities.translateToAminoAcidSequence(codonSequence, 0, codonSequence.length - 1); //System.out.println("AminoAcid Sequence: " + new String(aminoAcidSequence)); double[] triplePreferenceForGene = aminoAcidTriplePreference.calculateTriplePreferenceVectorNoNormalization(aminoAcidSequence); for (int i = 0; i < 8000; i++) { triplePreferenceArray[i] = triplePreferenceArray[i] + triplePreferenceForGene[i]; sum = sum + triplePreferenceForGene[i]; } currentCodonSequenceBuffer.delete(0,currentCodonSequenceBuffer.length()); } // gene doesn't continue geneCount = geneCount + 1; } } // for each segment in multisegment // normalize and output triple preference vector for (int i =0 ;i < 8000; i++) { triplePreferenceArray[i] = triplePreferenceArray[i] / sum; } PrintWriter outputWriter = new PrintWriter(new FileWriter(outputFileName)); for (int i = 0; i < 8000; i++) { if (i == 7999) outputWriter.println(triplePreferenceArray[i]); else outputWriter.print(triplePreferenceArray[i] + " "); } outputWriter.flush(); outputWriter.close(); } }