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| import java.io.*; | |
| import java.util.Vector; | |
| public class CRISPRFinder | |
| { | |
| private String inputFileName; | |
| private String outputFileName; | |
| private int screenDisplay; | |
| private int minNumRepeats; | |
| private int minRepeatLength; | |
| private int maxRepeatLength; | |
| private int minSpacerLength; | |
| private int maxSpacerLength; | |
| private int searchWindowLength; | |
| private int outputformat; | |
| private boolean printSpacers; | |
| private PrintStream spacers; | |
| private boolean printGffHeader; | |
| DNASequence sequence = null; | |
| int sequenceLength = 0; | |
| private int totalCrisprCount = 0; | |
| public CRISPRFinder(String _inputFileName, | |
| String _outputFileName, | |
| int _screenDisplay, | |
| int _minNumRepeats, | |
| int _minRepeatLength, | |
| int _maxRepeatLength, | |
| int _minSpacerLength, | |
| int _maxSpacerLength, | |
| int _searchWindowLength, | |
| int _outputformat, | |
| boolean _spacers) | |
| { | |
| inputFileName = _inputFileName; | |
| outputFileName = _outputFileName; | |
| screenDisplay = _screenDisplay; | |
| minNumRepeats = _minNumRepeats; | |
| minRepeatLength = _minRepeatLength; | |
| maxRepeatLength = _maxRepeatLength; | |
| minSpacerLength = _minSpacerLength; | |
| maxSpacerLength = _maxSpacerLength; | |
| searchWindowLength = _searchWindowLength; | |
| outputformat = _outputformat; | |
| printSpacers = _spacers; | |
| printGffHeader = true; | |
| if(_spacers) { | |
| File outputFile; | |
| FileOutputStream outputFileStream; | |
| if(_outputFileName == "") { | |
| String input_file_prefix = removeExtention(inputFileName); | |
| outputFile = new File(input_file_prefix + "_spacers.fa"); | |
| } else { | |
| String input_file_prefix = removeExtention(outputFileName); | |
| outputFile = new File(input_file_prefix + "_spacers.fa"); | |
| } | |
| try { | |
| outputFileStream = new FileOutputStream(outputFile, false); | |
| spacers = new PrintStream(outputFileStream); | |
| } catch (FileNotFoundException e) { | |
| // TODO Auto-generated catch block | |
| e.printStackTrace(); | |
| } | |
| } | |
| } | |
| private static String removeExtention(String filePath) { | |
| // These first few lines the same as Justin's | |
| File f = new File(filePath); | |
| // if it's a directory, don't remove the extention | |
| if (f.isDirectory()) return filePath; | |
| String name = f.getName(); | |
| // Now we know it's a file - don't need to do any special hidden | |
| // checking or contains() checking because of: | |
| final int lastPeriodPos = name.lastIndexOf('.'); | |
| if (lastPeriodPos <= 0) | |
| { | |
| // No period after first character - return name as it was passed in | |
| return filePath; | |
| } | |
| else | |
| { | |
| // Remove the last period and everything after it | |
| File renamed = new File(f.getParent(), name.substring(0, lastPeriodPos)); | |
| return renamed.getPath(); | |
| } | |
| } | |
| public boolean goCRISPRFinder() | |
| { | |
| File inputFile = new File(inputFileName); | |
| if (! inputFile.exists()) | |
| { | |
| System.err.println("File name does not exist: " + inputFile.getPath()); | |
| return false; | |
| } | |
| //System.out.println("\n\nReading file '" + inputFile.getPath() + "'"); | |
| FASTAReader fastaReader = new FASTAReader(inputFile.getPath()); | |
| if (! fastaReader.isFASTA()) | |
| { | |
| System.err.println("File '" + inputFile.getPath() + "' does not seem to be FASTA-formatted."); | |
| return false; | |
| } | |
| while ( fastaReader.read() ) | |
| { | |
| sequence = new DNASequence(fastaReader.getSequence(), fastaReader.getName(), fastaReader.getDesc()); | |
| //System.out.println("Sequence '" + sequence.getName() + "' (" + sequence.length() + " bp)"); | |
| /* | |
| // Check that sequence is a valid DNA sequence | |
| if ( ! sequence.isDNASequence() ) | |
| { | |
| System.out.println(sequence.getErrorLog() + "Skipping this sequence!"); | |
| System.out.println(""); | |
| continue; | |
| } | |
| */ | |
| sequence.mask(100); | |
| try | |
| { | |
| findRepeats(sequence, fastaReader.getNum()); | |
| } | |
| catch (Exception e) | |
| { | |
| System.err.println ("Error processing input file '" + inputFile.getPath() + "'. Please, check contents.\n"); | |
| } | |
| } | |
| //System.out.println("Done!"); | |
| return true; | |
| } | |
| private boolean findRepeats( DNASequence sequence, int readNum ) | |
| { | |
| Vector<CRISPR> CRISPRVector = new Vector<CRISPR>(); | |
| sequenceLength = sequence.length(); | |
| int actualRepeatLength; | |
| boolean repeatsFound = false; | |
| CRISPR candidateCRISPR; | |
| String pattern; | |
| if ((searchWindowLength < 6) || (searchWindowLength > 9)) | |
| { | |
| // Change window length | |
| int oldSearchWindowlength = searchWindowLength; | |
| searchWindowLength = 8; | |
| System.err.println("Changing window length to " + searchWindowLength + " instead of " + oldSearchWindowlength); | |
| } | |
| double spacerToSpacerMaxSimilarity = 0.62; | |
| int spacerToSpacerLengthDiff = 12; | |
| int spacerToRepeatLengthDiff = 30; | |
| //the mumber of bases that can be skipped while we still guarantee that the entire search | |
| //window will at some point in its iteration thru the sequence will not miss a any repeat | |
| int skips = minRepeatLength - (2 * searchWindowLength - 1); | |
| if (skips < 1) | |
| skips = 1; | |
| //System.out.println("Searching for repeats..."); | |
| long repeatSearchStart = System.currentTimeMillis(); | |
| SearchUtil searchUtil = new SearchUtil(); | |
| int searchEnd = sequenceLength - maxRepeatLength - maxSpacerLength - searchWindowLength; | |
| for (int j = 0; j <= searchEnd; j = j + skips) | |
| { | |
| candidateCRISPR = new CRISPR(); | |
| int beginSearch = j + minRepeatLength + minSpacerLength; | |
| int endSearch = j + maxRepeatLength + maxSpacerLength + searchWindowLength; | |
| if (endSearch > sequenceLength) | |
| endSearch = sequenceLength; | |
| if (endSearch < beginSearch) //should never occur | |
| endSearch = beginSearch; | |
| int mask_end = sequence.masked(beginSearch, endSearch); | |
| if(mask_end != -1) | |
| { | |
| j = mask_end; | |
| continue; | |
| } | |
| String text = sequence.substring(beginSearch, endSearch); | |
| pattern = sequence.substring(j, j + searchWindowLength); | |
| //if pattern is found, add it to candidate list and scan right for additional similarly spaced repeats | |
| int patternInTextIndex = searchUtil.boyer_mooreSearch(text, pattern); | |
| if (patternInTextIndex >= 0) | |
| { | |
| candidateCRISPR.addRepeat(j); | |
| candidateCRISPR.addRepeat(beginSearch + patternInTextIndex); | |
| candidateCRISPR = CRISPRUtil.scanRight(candidateCRISPR, pattern, minSpacerLength, 24, searchUtil); | |
| } | |
| if ( (candidateCRISPR.numRepeats() >= minNumRepeats) ) //make sure minNumRepeats is always at least 2 | |
| { | |
| candidateCRISPR = CRISPRUtil.getActualRepeatLength(candidateCRISPR, searchWindowLength, minSpacerLength); | |
| actualRepeatLength = candidateCRISPR.repeatLength(); | |
| if ( (actualRepeatLength >= minRepeatLength) && (actualRepeatLength <= maxRepeatLength) ) | |
| { if (CRISPRUtil.hasNonRepeatingSpacers(candidateCRISPR, spacerToSpacerMaxSimilarity)) | |
| { | |
| if (CRISPRUtil.hasSimilarlySizedSpacers(candidateCRISPR, spacerToSpacerLengthDiff, spacerToRepeatLengthDiff)) | |
| { | |
| candidateCRISPR = CRISPRUtil.checkFlank("left", candidateCRISPR, minSpacerLength, 30, spacerToSpacerMaxSimilarity, .70); | |
| candidateCRISPR = CRISPRUtil.checkFlank("right", candidateCRISPR, minSpacerLength, 30, spacerToSpacerMaxSimilarity, .70); | |
| candidateCRISPR = CRISPRUtil.trim(candidateCRISPR, minRepeatLength); | |
| CRISPRVector.addElement(candidateCRISPR); | |
| repeatsFound = true; | |
| //we may skip current CRISPR (assuming CRISPRs are not interleaved) | |
| j = candidateCRISPR.end() + 1; | |
| } | |
| } | |
| } | |
| } | |
| } | |
| long repeatSearchEnd = System.currentTimeMillis(); | |
| //System.out.println("Time to search for repeats: " + (repeatSearchEnd - repeatSearchStart) + " ms"); | |
| //System.out.println(CRISPRVector.size() + " possible CRISPR(s) found" + "\n"); | |
| // ********************** Display CRISPR elements ********************** // | |
| // ********************************************************************* // | |
| try | |
| { | |
| FileOutputStream outputFileStream; | |
| PrintStream out; | |
| if (screenDisplay == 1) | |
| out = System.out; | |
| else | |
| { | |
| if ( outputFileName.equals("") ) | |
| outputFileName = "a.out"; | |
| //System.out.println("Writing results in file '" + outputFileName + "'"); | |
| //System.out.println(""); | |
| File outputFile = new File(outputFileName); | |
| if ( readNum == 1 && outputFile.exists() ) | |
| { | |
| boolean success = outputFile.delete(); | |
| if (!success) | |
| throw new IllegalArgumentException("Error: Could not delete file '" + outputFile + "'"); | |
| } | |
| outputFileStream = new FileOutputStream(outputFile, true); | |
| out = new PrintStream(outputFileStream); | |
| } | |
| if (repeatsFound) | |
| { | |
| if(outputformat == 0) { | |
| out.print("Sequence '" + sequence.getName() + "' (" + sequence.length() + " bp)\n"); | |
| out.print("\n"); | |
| } else { | |
| if(printGffHeader) { | |
| out.println("##gff-version 3"); | |
| printGffHeader = false; | |
| } | |
| } | |
| //int repeatLength, numRepeats, numSpacers; | |
| CRISPR currCRISPR; | |
| //String repeat, spacer, prevSpacer; | |
| //repeat = spacer = prevSpacer = ""; | |
| //add 1 to each position, to offset programming languagues that begin at 0 rather than 1 | |
| for (int k = 0; k < CRISPRVector.size(); k++) | |
| { | |
| currCRISPR = (CRISPR)CRISPRVector.elementAt(k); | |
| if(outputformat > 0) { | |
| String crispr_id = "CRISPR" + (++totalCrisprCount); | |
| out.print(sequence.getName() + "\tminced:" + minced.VERSION + "\tCRISPR\t"); | |
| out.print((currCRISPR.start() + 1) + "\t" + (currCRISPR.end() + 1) + "\t"); | |
| out.print(currCRISPR.numRepeats() + "\t.\t.\tID="+ crispr_id); | |
| out.print("\n"); | |
| if(outputformat == 2) { | |
| out.print(currCRISPR.toGff(sequence.getName(), crispr_id)); | |
| } | |
| } else { | |
| out.print("CRISPR " + (++totalCrisprCount) + " Range: " + (currCRISPR.start() + 1) + " - " + (currCRISPR.end() + 1) + "\n"); | |
| out.print(currCRISPR.toString()); | |
| out.print("Repeats: " + currCRISPR.numRepeats() + "\t" + "Average Length: " + currCRISPR.averageRepeatLength() + "\t\t"); | |
| out.print("Average Length: " + currCRISPR.averageSpacerLength() + "\n\n"); | |
| } | |
| if(printSpacers) { | |
| for (int i = 0; i < currCRISPR.numSpacers(); ++i) { | |
| spacers.print(">"+ sequence.getName() +"_CRISPR_"+ (totalCrisprCount) +"_spacer_"+ (i+1)+"\n" + currCRISPR.spacerStringAt(i) + "\n"); | |
| } | |
| } | |
| } | |
| if(outputformat == 0) { | |
| out.print("Time to find repeats: " + (repeatSearchEnd - repeatSearchStart) + " ms\n\n"); | |
| out.print("\n"); | |
| } | |
| } | |
| if (screenDisplay == 0) | |
| out.close(); | |
| } | |
| catch (Exception e) { System.err.println ("--Error writing to file-- \n"); } | |
| return true; | |
| } | |
| } |