net.maizegenetics.analysis.rna.LoadRNAContigsToGBSDBPlugin Maven / Gradle / Ivy

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package net.maizegenetics.analysis.rna;



import net.maizegenetics.dna.tag.Tag;
import net.maizegenetics.dna.tag.TagBuilder;
import net.maizegenetics.dna.tag.TagDataSQLite;
import net.maizegenetics.dna.tag.TagDataWriter;
import net.maizegenetics.plugindef.*;
import net.maizegenetics.util.Utils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;

import javax.swing.*;
import java.awt.*;
import java.io.BufferedReader;

import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.HashMap;
import java.util.Map;


/**
 * Develops a discovery TBT file from a set of GBS sequence files.
 *
 * Keeps only good reads having a barcode and a cut site and no N's in the
 * useful part of the sequence. Trims off the barcodes and truncates sequences
 * that (1) have a second cut site, or (2) read into the common adapter.
 *
 * Originally the reference throughout was to "tag". This is being changed
 * to "kmer" as the pipeline is a kmer alignment process.
 *
 * @author Ed Buckler
 */
public class LoadRNAContigsToGBSDBPlugin extends AbstractPlugin {

    private static final Logger myLogger = LogManager.getLogger(LoadRNAContigsToGBSDBPlugin.class);

    private PluginParameter myContigFile = new PluginParameter.Builder<>("i", null, String.class).guiName("Input Fasta Contig File").required(true).inFile()
            .description("Input file containing contigs in fasta format.\n").build();
    private PluginParameter myOutputDB = new PluginParameter.Builder<>("db", null, String.class).guiName("Output Database File").required(true).outFile()
            .description("Output Database File").build();
    private PluginParameter myDeleteOldData = new PluginParameter.Builder<>("deleteOldData",false,Boolean.class).guiName("Delete Old Data")
            .description("Delete existing SNP quality data from db tables").build();

    public LoadRNAContigsToGBSDBPlugin() {
        super(null, false);
    }

    public LoadRNAContigsToGBSDBPlugin(Frame parentFrame, boolean isInteractive) {
        super(parentFrame, isInteractive);
    }

    @Override
    protected void preProcessParameters(DataSet input) {
        super.preProcessParameters(input);
        if (Files.exists(Paths.get(outputDB()))) {
            if (deleteOldData()) {
                try {
                    Files.delete(Paths.get(myOutputDB.value()));
                } catch (Exception exc) {
                    System.out.println("Error when trying to delete database file: " + myOutputDB.value());
                    System.out.println("File delete error: " + exc.getMessage());
                }
            }
        }
    }

    @Override
    public DataSet processData(DataSet input) {
        long lineNumber=0;

        try {
            TagDataWriter tdw =new TagDataSQLite(myOutputDB.value());
            BufferedReader br = Utils.getBufferedReader(contigFile(), 1 << 22);
            String line;
            String header=null;
            StringBuilder seq=new StringBuilder();
            Map contigNameMap=new HashMap<>(100_000);
            while ((line = br.readLine())!= null) {
                line = line.trim();
                lineNumber++;
                if (line.startsWith(">")) {
                    if(header!=null) {
                        Tag newTag = TagBuilder.instance(seq.toString()).build();
                        // Tag is null if sequence contains anything other than A,G,C,T
                        // Also null:  A tag consisting of 32 T's becomes -1 in "getLongFromSequence", 
                        // which results in a "null" tag (seen in the Zea_mays.AGPv3 chromosome files
                        // when running GBSv2 SAMToGBSdbPlugin) 
                        if (newTag != null) {
                            contigNameMap.put(newTag, header);
                        } else {
                            // System.out.println("LoadRNAContigsToGBSDBPlugin: processData, NULL tag for sequence: " + seq.toString());  
                        }
                    }
                    //reset to new sequence
                    header=line;
                    seq=new StringBuilder();
                } else {
                    seq.append(line);
                }
            }
            if(header!=null) {
                Tag newTag = TagBuilder.instance(seq.toString()).build();
                if (newTag != null) {
                    contigNameMap.put(newTag,header);
                }
                
            }
            tdw.putAllNamesTag(contigNameMap);  //add map to databse
            ((TagDataSQLite)tdw).close();

        } catch(Exception ioe) {
            System.err.println("Error in line number "+lineNumber);
            ioe.printStackTrace();
        }
        return new DataSet(new Datum("OutputDatabase",outputDB(),""),this);
    }




// The following getters and setters were auto-generated.
    // Please use this method to re-generate.
    //
//     public static void main(String[] args) {
//         GeneratePluginCode.generate(LoadRNAContigsToGBSDB.class);
//     }

    /**
     * Convenience method to run plugin with one return object.
     */
    // TODO: Replace  with specific type.
    public String runPlugin(DataSet input) {
        return (String) performFunction(input).getData(0).getData();
    }

    /**
     * Input file containing contigs in fasta format.
     *
     *
     * @return Input Fasta Contig File
     */
    public String contigFile() {
        return myContigFile.value();
    }

    /**
     * Set Input Fasta Contig File. Input file containing
     * contigs in fasta format.
     *
     *
     * @param value Input Fasta Contig File
     *
     * @return this plugin
     */
    public LoadRNAContigsToGBSDBPlugin contigFile(String value) {
        myContigFile = new PluginParameter<>(myContigFile, value);
        return this;
    }

    /**
     * Output Database File
     *
     * @return Output Database File
     */
    public String outputDB() {
        return myOutputDB.value();
    }

    /**
     * Set Output Database File. Output Database File
     *
     * @param value Output Database File
     *
     * @return this plugin
     */
    public LoadRNAContigsToGBSDBPlugin outputDB(String value) {
        myOutputDB = new PluginParameter<>(myOutputDB, value);
        return this;
    }

    /**
     * Delete existing SNP quality data from db tables
     *
     * @return Delete Old Data
     */
    public Boolean deleteOldData() {
        return myDeleteOldData.value();
    }

    /**
     * Set Delete Old Data. Delete existing SNP quality data
     * from db tables
     *
     * @param value Delete Old Data
     *
     * @return this plugin
     */
    public LoadRNAContigsToGBSDBPlugin deleteOldData(Boolean value) {
        myDeleteOldData = new PluginParameter<>(myDeleteOldData, value);
        return this;
    }


    @Override
    public ImageIcon getIcon() {
        return null;
    }

    @Override
    public String getButtonName() {
        return null;
    }

    @Override
    public String getToolTipText() {
        return null;
    }
}