minced.java

import java.io.*;

public class minced
{
   public static final String VERSION = "0.2.0";
	public static void main(String[] args)
   {
      //default values
      int screenDisplay      = 1;
      int minNumRepeats      = 3;
      int minRepeatLength    = 23;
      int maxRepeatLength    = 47;
      int minSpacerLength    = 26;
      int maxSpacerLength    = 50;
      int searchWindowLength = 8;
      boolean spacers        = false;
      // set the output format
      // 0 = original report
      // 1 = summary gff
      // 2 = full gff
      int outformat = 0;

      int numOptions = 0;

      if (args.length == 0)
      {
         printUsage();
         //System.out.println("No arguments specified.");
         //System.out.println("Try 'minced --help' for more information.");
         System.exit(1);
      }

      if (args[0].equals("--help") || args[0].equals("-h"))
      {
         printUsage();
         System.exit(1);
      }

      if (args[0].equals("--version"))
      {
         printVersion();
         System.exit(0);
      }

      int i = 0;
      while (args[i].charAt(0) == '-')
      {
         try
         {
            if (args[i].endsWith("minNR"))
            {
               i++;
               if (i >= args.length)
               {
                  System.out.println("Missing option value for " + args[i - 1] + ".");
                  System.out.println("Try 'minced --help' for more information.");
                  System.exit(1);
               }
               minNumRepeats = Integer.parseInt(args[i]);
               numOptions += 2;
            }
            else if (args[i].endsWith("gff")) {
            	outformat = 1;
            	numOptions++;
            }
            else if (args[i].endsWith("gffFull")) {
            	outformat = 2;
            	numOptions++;
            }
            else if (args[i].endsWith("spacers")) {
            	spacers = true;
            	numOptions++;
            }
            else if (args[i].endsWith("minRL"))
            {
               i++;
               if (i >= args.length)
               {
                  System.out.println("Missing option value for " + args[i - 1] + ".");
                  System.out.println("Try 'minced --help' for more information.");
                  System.exit(1);
               }
               minRepeatLength = Integer.parseInt(args[i]);
               numOptions +=2;
            }
            else if (args[i].endsWith("maxRL"))
            {
               i++;
               if (i >= args.length)
               {
                  System.out.println("Missing option value for " + args[i - 1] + ".");
                  System.out.println("Try 'minced --help' for more information.");
                  System.exit(1);
               }
               maxRepeatLength = Integer.parseInt(args[i]);
               numOptions += 2;
            }
            else if (args[i].endsWith("minSL"))
            {
               i++;
               if (i >= args.length)
               {
                  System.out.println("Missing option value for " + args[i - 1] + ".");
                  System.out.println("Try 'minced --help' for more information.");
                  System.exit(1);
               }
               minSpacerLength = Integer.parseInt(args[i]);
               numOptions += 2;
            }
            else if (args[i].endsWith("maxSL"))
            {
               i++;
               if (i >= args.length)
               {
                  System.out.println("Missing option value for " + args[i - 1] + ".");
                  System.out.println("Try 'minced --help' for more information.");
                  System.exit(1);
               }
               maxSpacerLength = Integer.parseInt(args[i]);
               numOptions += 2;
            }
            else if (args[i].endsWith("searchWL"))
            {
               i++;
               if (i >= args.length)
               {
                  System.out.println("Missing option value for " + args[i - 1] + ".");
                  System.out.println("Try 'minced --help' for more information.");
                  System.exit(1);
               }
               searchWindowLength = Integer.parseInt(args[i]);
               numOptions += 2;
               if ( (searchWindowLength < 6) || (searchWindowLength > 9) )
               {
                  searchWindowLength = 8;
                  System.out.println("--Reseting search window length to " + searchWindowLength + "--");
               }
            }
            /*
            else if (args[i].endsWith("screen"))
            {
               i++;
               if (i >= args.length)
               {
                  System.out.println("Missing option value for " + args[i - 1] + ".");
                  System.out.println("Try 'minced --help' for more information.");
                  System.exit(1);
               }
               screenDisplay = Integer.parseInt(args[i]);
               numOptions++;
               if ( screenDisplay != 1 )
                  screenDisplay = 0;
            }
            */
            else
            {
               System.out.println("Invalid option:  " + args[i]);
               System.out.println("Try 'minced --help' for more information.");
               System.exit(1);
            }
            i++;  //--------//
            if (i >= args.length)
            {
               System.out.println("No input file specified.");
               System.out.println("Try 'minced --help' for more information.");
               System.exit(1);
            }
         }  //end try
         catch (NumberFormatException e) // exception will be caught if user does not specify an integer after each option
         {
            System.out.println("Invalid argument type.  Please, specify an option followed by an integer.  For example:  -minNR 3");
            System.out.println("Try 'minced --help' for more information.");
            System.exit(1);
         }
      }  // end while


      // Last options should be an input file and optional output file
      String inputFileName = "";
      String outputFileName = "";
      boolean outputFileSpecified = false;
      int numArgsRemaining = args.length - numOptions;

      if (numArgsRemaining == 1)
         inputFileName = args[i];
      else if (numArgsRemaining == 2)
      {
         inputFileName = args[i];
         outputFileSpecified = true;
         outputFileName = args[i + 1];
         screenDisplay = 0;
      }
      else
      {
         System.out.println("Improper usage.");
         System.out.println("Try 'minced --help' for more information.");
         System.exit(1);
      }


      File inputFile = new File(inputFileName);
      if (!inputFile.exists())
      {
         System.out.println("Input file " + inputFile.getPath() + " does not exist.");
         System.exit(1);
      }

      if (inputFile.isDirectory())
      {
         System.out.println("You have entered a directory name. An input file name is required: " + inputFile.getPath());
         System.exit(1);
      }



      File outputFile;
      if (outputFileSpecified)
      {
         outputFile = new File(outputFileName);

         if (outputFile.isDirectory())
         {
            System.out.println("You have entered an existing directory name. An output file name is required: " + outputFile.getAbsolutePath());
            System.exit(1);
         }

         if (!outputFile.getAbsoluteFile().getParentFile().isDirectory())
         {
            System.out.println("You did not enter a valid file output path: " + outputFile.getAbsolutePath());
            System.exit(1);
         }
      }


      CRISPRFinder client = new CRISPRFinder(inputFileName,
    		  outputFileName,
    		  screenDisplay,
    		  minNumRepeats,
    		  minRepeatLength,
    		  maxRepeatLength,
    		  minSpacerLength,
    		  maxSpacerLength,
    		  searchWindowLength,
    		  outformat,
    		  spacers);
      client.goCRISPRFinder();

   }

   public static void printUsage()
   {
      System.out.println("MinCED, a program to find CRISPRs in shotgun DNA sequences or full genomes");
      System.out.println();
      System.out.println("Usage:    minced [options] file.fa [outputFile]");
      System.out.println();
      System.out.println("Options:  -searchWL  Length of search window used to discover CRISPRs (range: 6-9). Default: 8");
      System.out.println("          -minNR     Minimum number of repeats a CRISPR must contain. Default: 3");
      System.out.println("          -minRL     Minimum length of the CRISPR repeats. Default: 23");
      System.out.println("          -maxRL     Maximum length of the CRISPR repeats. Default: 47");
      System.out.println("          -minSL     Minimum length of the CRISPR spacers. Default: 26");
      System.out.println("          -maxSL     Maximum length of the CRISPR spacers. Default: 50");
      System.out.println("          -gff       Output summary results in gff format containing");
      System.out.println("                     only the positions of the CRISPR arrays. Default: false");
      System.out.println("          -gffFull   Output detailed results in gff format containing");
      System.out.println("                     positions of CRISPR arrays and all repeat units. Default: false");
      System.out.println("          -spacers   Output a fasta formatted file containing the spacers. Default: false");
      System.out.println("          -h --help  Output this handy help message");
      System.out.println("          --version  Output version information");
      System.out.println();
      System.out.println("Examples: minced ecoli.fna");
      System.out.println("          minced -minNR 2 metagenome.fna");
      System.out.println("          minced -minNR 2 metagenome.fna metagenome.crisprs");
      System.out.println();
   }

   public static void printVersion()
   {
      System.out.println("minced " + VERSION);
	   System.out.println("MinCED - Mining CRISPRs in Environmental Datasets (version " + VERSION + ")");
      System.out.println("Copyright 2011      Florent Angly     <florent.angly@gmail.com>");
      System.out.println("          2013-2015 Connor Skennerton <c.skennerton@gmail.com>");
      System.out.println();
      System.out.println("Minced is a modified version of CRT (www.room220.com/crt)");
      System.out.println("Charles Bland et al., CRISPR Recognition Tool (CRT): a tool for automatic");
      System.out.println("detection of clustered regularly interspaced palindromic repeats");
      System.out.println("BMC Bioinformatics 8, no. 1 (2007): 209.");
      System.out.println("Distributed under the GNU General Public License version 3");
   }

}