eqtlmappingpipeline.mixupmapper.MixupMapperConsoleGUI Maven / Gradle / Ivy

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/*
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 * and open the template in the editor.
 */
package eqtlmappingpipeline.mixupmapper;

import umcg.genetica.console.ConsoleGUIElems;

/**
 *
 * @author harmjan
 */
public class MixupMapperConsoleGUI {

    public MixupMapperConsoleGUI(String[] args) {


        String xmlSettingsFile = null;
        String settingstexttoreplace = null;
        String settingstexttoreplacewith = null;
        String in = null;
        String out = null;
        boolean cis = true;
        boolean trans = false;
        int perm = 10;
        String outtype = "text";
        String inexp = null;
        String inexpplatform = null;
        String inexpannot = null;
        String gte = null;
        Integer threads = null;
        String inputeQTLs = null;
        String snps = null;
        boolean allCombos = false;

        for (int i = 0; i < args.length; i++) {
            String arg = args[i];
            String val = null;

            if (i + 1 < args.length) {
                val = args[i + 1];
            }

            if (arg.equals("--in")) {
                in = val;
            } else if (arg.equals("--out")) {
                out = val;
            } else if (arg.equals("--inexp")) {
                inexp = val;
            } else if (arg.equals("--inexpplatform")) {
                inexpplatform = val;
            } else if (arg.equals("--inexpannot")) {
                inexpannot = val;
            } else if (arg.equals("--snps")) {
                snps = val;
            } else if (arg.equals("--gte")) {
                gte = val;
            } else if (arg.equals("--eqtls")) {
                inputeQTLs = val;
            } else if (arg.equals("--testall")) {
                allCombos = true;
            } else if (arg.equals("--perm")) {
                try {
                    perm = Integer.parseInt(val);
                } catch (NumberFormatException e) {
                    System.out.println("Please supply an integer for --perm");
                }
            } else if (arg.equals("--threads")) {
                try {
                    threads = Integer.parseInt(val);
                } catch (NumberFormatException e) {
                    System.err.println("Error --threads should be an integer");
                }

            }
        }

        try {
            if (in == null || out == null) {
                System.out.println("ERROR: Please supply settings --in and --out");
                printUsage();
            } else {
                MixupMapper m = new MixupMapper();
                m.run(xmlSettingsFile, settingstexttoreplace, settingstexttoreplacewith, in, inexp, inexpplatform, inexpannot, gte, out, cis, trans, perm, true, false, snps, threads, 500000, null, null, inputeQTLs, allCombos);
            }
        } catch (Exception e) {
            e.printStackTrace();
            System.exit(-1);
        }
    }

    private void printUsage() {
        System.out.print("Command line options:\n" + ConsoleGUIElems.LINE);
        System.out.println("--in\t\t\tdir\t\tLocation of the genotype data\n"
                + "--out\t\t\tdir\t\tLocation where the output should be stored\n"
                + "--inexp\t\t\tstring\t\tLocation of expression data\n"
                + "--inexpplatform\t\tstring\t\tGene expression platform\n"
                + "--inexpannot\t\tstring\t\tLocation of annotation file for gene expression data\n"
                + "--gte\t\t\tstring\t\tLocation of genotype to expression coupling file\n"
                + "--perm\t\t\tstring\t\tNumber of permutations to perform in order to determine FDR\n"
                + "--eqtls\t\t\tstring\t\tPath to eQTL file to use for MixupMapper\n"
                + "--testall\t\t\t\tTest all possible combinations of genotype and gene expression samples\n"
                + "--threads\t\tinteger\t\tNumber of threads to calculate with. Default is number of processors.\n"
                + "--snps\t\tstring\t\tList of SNPs to test.");
        System.out.println("");
    }
}