https://github.com/ctSkennerton/minced
minced.java
import java.io.*;
public class minced
{
public static final String VERSION = "0.3.2";
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(" 2013-2018 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");
}
}
