Example usage for java.io Reader toString

List of usage examples for java.io Reader toString

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Introduction

In this page you can find the example usage for java.io Reader toString.

Prototype

public String toString()

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Document

Returns a string representation of the object.

Usage

From source file:org.intermine.bio.dataconversion.XenmineConverter.java

/**
 * //from  w  w  w .  ja va2s .  c o  m
 * @param reader
 * @throws Exception
 * @throws ObjectStoreException
 */
private void processInteractionsFile(Reader preader) throws Exception, ObjectStoreException {

    /* Xenbase gene ID      
     * gene symbol     
     *  interactant ID:interactant symbol:co-citation occurrence
     */
    System.out.println("Processing Interactants file....");

    Iterator<?> tsvIter;
    try {
        tsvIter = FormattedTextParser.parseTabDelimitedReader(preader);
    } catch (Exception e) {
        throw new Exception("cannot parse file: " + preader.toString(), e);
    }

    while (tsvIter.hasNext()) {

        String[] line = (String[]) tsvIter.next();

        if (line.length < 3) {
            LOG.error("Couldn't process line. Expected 3 cols, but was " + line.length);
            continue;
        }

        String genePageId = line[0].trim().substring(12);
        String symbol = line[1].trim();
        String interactants = line[2].trim(); //genePageId-PMID:symbol:someNumber   

        if (interactants == null || interactants.length() == 0 || interactants.equals("")) {
            continue;
        }
        String[] interactingGenes = interactants.split(",");

        //System.out.println("Gene Page.."+ genePageId + "  Length of inG.." + interactingGenes.length);

        HashSet geneIds = genesPageName.get(genePageId);
        Iterator it = geneIds.iterator();

        while (it.hasNext()) {

            String geneId = (String) it.next();
            Item gene = genes.get(geneId);

            if (interactingGenes.length != 0) {

                for (int i = 0; i < interactingGenes.length; i++) {

                    String gpid[] = interactingGenes[i].split("\\:");
                    String genePageIdInteractant = gpid[0];

                    //System.out.println("gene interactant.." + genePageIdInteractant);

                    HashSet interactingGeneIds = genesPageName.get(genePageIdInteractant);
                    if (interactingGeneIds == null) {
                        continue;
                    }
                    Iterator itt = interactingGeneIds.iterator();

                    while (itt.hasNext()) {

                        String interactingGeneId = (String) itt.next();
                        Item interactingGene = genes.get(interactingGeneId);

                        if (gene != null && interactingGene != null) {
                            getInteraction(gene.getIdentifier(), interactingGene.getIdentifier());
                        }
                    }

                }

            }
        }

    }

    preader.close();

}

From source file:org.intermine.bio.dataconversion.XenmineConverter.java

/**
 * //from w w  w .j  a  va2s.c  o m
 * @param reader
 * @throws Exception
 * @throws ObjectStoreException
 */

private void processExpressionFile(Reader preader) throws Exception, ObjectStoreException {

    /* Xenbase Gene ID - XB-GENE-865139   
     * Symbol -  nr5a2-a   
     * Genotype - wild type   
     * Anatomical Tissue - XAO:0000132 liver and biliary system,XAO:0000467 dorsal pancreatic bud,XAO:0001103 ventral pancreatic bud,XAO:0003266 liver primordium   
     * Start Stage - XAO:1000049 NF stage 35 and 36   
     * End Stge - XAO:1000053 NF stage 41   
     * assay - in situ hybridization   
     * EvidenceID - Image - XB-IMG-26168   
     * Expreriment ID - XB-EXP-6382   
     * Source - Published   
     * Literature ID - XB-ART-39030   
     * Curation Status - Complete manual curation
     */

    System.out.println("Processing Expression file....");

    Iterator<?> tsvIter;
    try {
        tsvIter = FormattedTextParser.parseTabDelimitedReader(preader);
    } catch (Exception e) {
        throw new Exception("cannot parse file: " + preader.toString(), e); //getCurrentFile()
    }

    while (tsvIter.hasNext()) {

        String[] line = (String[]) tsvIter.next();

        if (line.length < 12) {
            LOG.error("Couldn't process line. Expected 12 cols, but was " + line.length);
            continue;
        }

        String xenbaseGeneId = line[0].trim();
        String symbol = line[1].trim();
        String genotype = line[2].trim();

        String anatomicalTissue = line[3].trim();
        String startStageFull = line[4].trim(); //XAO:1000049 NF stage 35 and 36
        String[] t = startStageFull.split("\\s");
        String startStage = t[0];

        String endStageFull = line[5].trim();
        String[] te = endStageFull.split("\\s");
        String endStage = te[0];

        String assay = line[6].trim();
        String imageId = line[7].trim();

        String experimentId = line[8].trim();
        String source = line[9].trim();

        String literatureId = line[10].trim(); //XB-ART-ID figure out how to merge based on PMID
        String pmid = pmid_xbartid.get(literatureId);
        String refId = getPub(pmid, literatureId);

        String status = line[11].trim();

        //figure out how to store this stuff
        Item expression = createItem("ExpressionResult");

        if (StringUtils.isNotEmpty(genotype)) {
            expression.setAttribute("genotype", genotype);
        }
        if (StringUtils.isNotEmpty(assay)) {
            expression.setAttribute("assay", assay);
        }
        if (StringUtils.isNotEmpty(experimentId)) {
            expression.setAttribute("experimentId", experimentId);
        }
        if (StringUtils.isNotEmpty(source)) {
            expression.setAttribute("source", source);
        }
        if (StringUtils.isNotEmpty(status)) {
            expression.setAttribute("curationStatus", status);
        }

        Item sterm = getTerm(startStage);
        Item eterm = getTerm(endStage);
        expression.setReference("startStage", sterm.getIdentifier());
        expression.setReference("endStage", eterm.getIdentifier());

        expression.setReference("publication", refId);

        setImage(expression, URL + imageId + ".jpg");

        setAnatomicalTissues(expression, anatomicalTissue, "anatomicalStages");

        Item gene = genes.get(xenbaseGeneId);
        if (gene != null) { //XB-GENE-478125 is not in other files
            expression.setReference("gene", gene.getIdentifier());
            store(expression); //don't store all other items created if there is no gene to associate with..?
        }

    }

    preader.close();

}

From source file:org.intermine.bio.dataconversion.XenmineConverter.java

/**
 * //from   ww w  .  j  a  v a2 s .  com
 * @param reader
 * @throws Exception
 * @throws ObjectStoreException
 */

private void processAnatomyMappingFile(Reader preader) throws Exception, ObjectStoreException {

    /* Xenbase Gene ID
     * gene symbol
     * start stage
     * end stage
     * tissues
     * XB-GENEPAGE-478053      trnt1   XAO:1000031 NF stage 10.5       XAO:1000009 frog       
     *  XAO:0000001 ectoderm,XAO:0003024 head,XAO:0000129 intestine,XAO:0000133 liver,XAO:0000256 oocyte,
     *  XAO:0000258 ovary,XAO:0000157 testis,XAO:0003004 whole organism
     */

    System.out.println("Processing Anatomy Mapping file....");

    Iterator<?> tsvIter;
    try {
        tsvIter = FormattedTextParser.parseTabDelimitedReader(preader);
    } catch (Exception e) {
        throw new Exception("cannot parse file: " + preader.toString(), e); //getCurrentFile()
    }

    while (tsvIter.hasNext()) {

        String[] line = (String[]) tsvIter.next();

        String xenbaseGeneId = line[0].trim().substring(12);
        String symbol = line[1].trim();
        String startStageFull = line[2].trim(); //XAO:1000049 NF stage 35 and 36
        String[] t = startStageFull.split("\\s");
        String startStage = t[0];
        String endStageFull = line[3].trim();
        String[] te = endStageFull.split("\\s");
        String endStage = te[0];
        String anatomicalTissue = line[4].trim();
        System.out.println(xenbaseGeneId);
        HashSet geneIds = genesPageName.get(xenbaseGeneId); //check this stuff with what is in genes..a thorough once over
        Iterator it = geneIds.iterator();
        while (it.hasNext()) {

            String geneId = (String) it.next();
            Item gene = genes.get(geneId);
            if (gene != null) {
                //figure out how to store this stuff
                Item anatomy = createItem("AnatomyMapping");
                Item sterm = getTerm(startStage);
                Item eterm = getTerm(endStage);
                anatomy.setReference("startStage", sterm.getIdentifier());
                anatomy.setReference("endStage", eterm.getIdentifier());
                setAnatomicalTissues(anatomy, anatomicalTissue, "tissues");
                anatomy.setReference("gene", gene.getIdentifier());
                store(anatomy); //don't store all other items created if there is no gene to associate with..?
            }
        }

    }

    preader.close();

}

From source file:org.intermine.bio.dataconversion.XenmineConverter.java

/**
 * //from  w w w  .ja  v a2s  .com
 * @param reader
 * @throws Exception
 * @throws ObjectStoreException
 */

private void processLiteratureFile(Reader preader) throws Exception, ObjectStoreException {

    /* Xenbase Literature ID      
     * PMID     
     *  Xenbase genePage IDs associated with the PMID above
     */

    System.out.println("Processing Literature file....");

    Iterator<?> tsvIter;
    try {
        tsvIter = FormattedTextParser.parseTabDelimitedReader(preader);
    } catch (Exception e) {
        throw new Exception("cannot parse file: " + preader.toString(), e); //getCurrentFile()
    }

    while (tsvIter.hasNext()) {

        String[] line = (String[]) tsvIter.next();

        if (line.length < 3) {
            LOG.error("Couldn't process line. Expected 3 cols, but was " + line.length);
            continue;
        }

        String literatureId = line[0].trim().substring(7);
        String pmid = line[1].trim();
        String litGenes = line[2].trim(); //XB-GENEPAGE-491748 elavl2,XB-GENEPAGE-481418 gdf1,XB-GENEPAGE-481799 elavl1      

        if (litGenes.isEmpty() || litGenes == null) {
            System.out.println("empty 3rd column.");
            continue;

        }

        String storedRefId = getPub(pmid, literatureId);

        String[] gids = litGenes.split(",");

        if (gids.length != 0) {
            for (int i = 0; i < gids.length; i++) {

                String gpid[] = gids[i].split("\\s");
                String genePageId = gpid[0].substring(12);

                HashSet geneIds = genesPageName.get(genePageId); //check this stuff with what is in genes..a thorough once over
                Iterator it = geneIds.iterator();
                while (it.hasNext()) {

                    String geneId = (String) it.next();
                    Item gene = genes.get(geneId);
                    if (gene != null) {
                        gene.addToCollection("publications", storedRefId);
                    }
                }

            }
        } else {

            String gpid[] = litGenes.split("\\s");
            String genePageId = gpid[0].substring(12);
            HashSet geneIds = genesPageName.get(genePageId); //check this stuff with what is in genes..a thorough once over
            Iterator it = geneIds.iterator();
            while (it.hasNext()) {

                String geneId = (String) it.next();
                Item gene = genes.get(geneId);
                if (gene != null) {
                    gene.addToCollection("publications", storedRefId);
                }
            }
        }

    }

    preader.close();

}

From source file:org.intermine.bio.dataconversion.XenmineConverter.java

/**
 * // ww  w .  ja  v a 2s  . c  o m
 * @param reader
 * @throws Exception
 * @throws ObjectStoreException
 */

private void processGoFile(Reader preader) throws Exception, ObjectStoreException {

    /* Xenbase genepage ID     
     * gene symbol     
     * GO Ids  (comma separated)
     */

    System.out.println("Processing GO file....");

    Iterator<?> tsvIter;
    try {
        tsvIter = FormattedTextParser.parseTabDelimitedReader(preader);
    } catch (Exception e) {
        throw new Exception("cannot parse file: " + preader.toString(), e); //getCurrentFile()
    }

    while (tsvIter.hasNext()) {

        String[] line = (String[]) tsvIter.next();

        if (line.length < 3) {
            LOG.error("Couldn't process line. Expected 3 cols, but was " + line.length);
            continue;
        }

        String genePageId = line[0].trim().substring(12);
        String symbol = line[1].trim();
        String goids = line[2].trim(); //GO:0005525,GO:0007264,GO:0015031

        HashSet geneIds = genesPageName.get(genePageId);
        if (geneIds == null) {
            System.out.println("genePageId: null for genes..");
            continue;
        }
        Iterator it = geneIds.iterator();
        while (it.hasNext()) {

            String geneId = (String) it.next();
            Item gene = genes.get(geneId);
            //System.out.println("genePageId: " + genePageId + " geneId " + geneId);
            String[] gids = goids.split(",");
            for (int i = 0; i < gids.length; i++) {
                String goTermIdentifier = gids[i];
                if (gene != null) {
                    createGoAnnotation(gene.getIdentifier(), gene, goTermIdentifier, "XenBase", "XenBase");
                }
            }

        }
    }

    preader.close();

}

From source file:org.intermine.bio.dataconversion.XenmineConverter.java

/**
 * /*  w w w.j a  v  a  2s .c  o m*/
 * @param reader
 * @throws Exception
 * @throws ObjectStoreException
 */
private void processEnsemblFile(Reader preader) throws Exception, ObjectStoreException {

    /* Xenbase gene ID     
     * gene symbol     
     * description
     * ENSXETG00000xxxx - ensembl ID
     */
    System.out.println("Processing Ensembl file....");

    Iterator<?> tsvIter;
    try {
        tsvIter = FormattedTextParser.parseTabDelimitedReader(preader);
    } catch (Exception e) {
        throw new Exception("cannot parse file: " + preader.toString(), e); //getCurrentFile()
    }

    while (tsvIter.hasNext()) {

        String[] line = (String[]) tsvIter.next();

        if (line.length < 4) {
            LOG.error("Couldn't process line. Expected 4 cols, but was " + line.length);
            continue;
        }

        String geneId = line[0].trim();
        String symbol = line[1].trim();
        String name = line[2].trim();
        String ensemblId = line[3].trim();

        Item gene = genes.get(geneId);
        if (gene != null && ensemblId != null) {
            gene.setAttribute("ensemblIdentifier", ensemblId);
        }

    }

    preader.close();

}

From source file:org.intermine.bio.dataconversion.XenmineConverter.java

/**
 * /* w  w  w.  j  a v a 2s  .c om*/
 * @param reader
 * @throws Exception
 * @throws ObjectStoreException
 */
private void processNonEntrezOrthologFile(Reader preader) throws Exception, ObjectStoreException {

    /* Xenbase 
     * OMIM    
     * MGI     
     * ZFIN
     */
    System.out.println("Processing  Non Entrze Orthologs.. XenbaseGeneNonEntrezOrthologMapping.txt file....");

    Iterator<?> tsvIter;
    try {
        tsvIter = FormattedTextParser.parseTabDelimitedReader(preader);
    } catch (Exception e) {
        throw new Exception("cannot parse file: " + preader.toString(), e);
    }

    String prevXenopusId = "";

    while (tsvIter.hasNext()) {

        String[] line = (String[]) tsvIter.next();

        if (line.length < 4) {
            LOG.error("Couldn't process line. Expected 4 cols, but was " + line.length);
            continue;
        }
        System.out.println(line[0].trim());

        String xenopusId = line[0].trim().substring(8); //it doesn;t say GENEPAGE!!
        String omimId = line[1].trim();
        String mgiId = line[2].trim();
        String zfinId = line[3].trim();
        String chickenId = line[4].trim();

        if (prevXenopusId == xenopusId) {

            HashSet geneIds = genesPageName.get(xenopusId);
            Iterator it = geneIds.iterator();

            while (it.hasNext()) {

                String geneId = (String) it.next();
                Item gene0 = genes.get(geneId);
                if (gene0 != null) {

                    if (!StringUtils.isEmpty(zfinId)) {
                        String gene3 = getGene(zfinId, "7955");
                        if (gene3 != null)
                            processHomologues(gene0.getIdentifier(), gene3);
                    }

                }

            }

        } else {

            HashSet geneIds = genesPageName.get(xenopusId);
            Iterator it = geneIds.iterator();

            while (it.hasNext()) {

                String geneId = (String) it.next();
                Item gene0 = genes.get(geneId);
                if (gene0 != null) {

                    if (!StringUtils.isEmpty(omimId)) {
                        String gene1 = getGene(omimId, "9606");
                        if (gene1 != null)
                            processHomologues(gene0.getIdentifier(), gene1);
                    }

                    if (!StringUtils.isEmpty(mgiId)) {
                        String gene2 = getGene(mgiId, "10090");
                        if (gene2 != null)
                            processHomologues(gene0.getIdentifier(), gene2);
                    }

                    if (!StringUtils.isEmpty(zfinId)) {
                        String gene3 = getGene(zfinId, "7955");
                        if (gene3 != null)
                            processHomologues(gene0.getIdentifier(), gene3);
                    }
                    if (!StringUtils.isEmpty(chickenId)) {
                        String gene4 = getGene(chickenId, "9031");
                        if (gene4 != null)
                            processHomologues(gene0.getIdentifier(), gene4);
                    }

                }

            }
        }

        prevXenopusId = xenopusId;

    }

    preader.close();

}

From source file:org.intermine.bio.dataconversion.XenmineConverter.java

/**
 * /*from   w  ww  .java2 s. c  om*/
 * @param reader
 * @throws Exception
 * @throws ObjectStoreException
 */
private void processZebrafishOrthologFile(Reader preader) throws Exception, ObjectStoreException {

    /* entrez/NCBI gene ID     
     * Xenbase GenePage     
     * symbol
     * name
     */
    System.out.println("Processing ZebraFish Ortholog file....");

    Iterator<?> tsvIter;
    try {
        tsvIter = FormattedTextParser.parseTabDelimitedReader(preader);
    } catch (Exception e) {
        throw new Exception("cannot parse file: " + preader.toString(), e);
    }

    while (tsvIter.hasNext()) {

        String[] line = (String[]) tsvIter.next();

        if (line.length < 4) {
            LOG.error("Couldn't process line. Expected 4 cols, but was " + line.length);
            continue;
        }

        String humanIdentifier = line[0].trim();
        String xenopusIdentifier = line[1].trim().substring(12);

        if (StringUtils.isEmpty(xenopusIdentifier) || StringUtils.isEmpty(humanIdentifier)) {
            continue;
        }

        String gene2 = getGene(humanIdentifier, "7955");

        HashSet geneIds = genesPageName.get(xenopusIdentifier);
        Iterator it = geneIds.iterator();

        while (it.hasNext()) {

            String geneId = (String) it.next();
            Item gene1 = genes.get(geneId);
            if (gene1 != null && gene2 != null) { //lot of trouble..why should this check be required..does not make sense..spend time debug
                processHomologues(gene1.getIdentifier(), gene2);
            }

        }

    }

    preader.close();

}

From source file:org.intermine.bio.dataconversion.XenmineConverter.java

/**
 * /*  ww w. j  ava 2 s  .c  o  m*/
 * @param reader
 * @throws Exception
 * @throws ObjectStoreException
 */
private void processHumanOrthologFile(Reader preader) throws Exception, ObjectStoreException {

    /* entrez/NCBI gene ID     
     * Xenbase GenePage     
     * symbol
     * name
     */
    System.out.println("Processing Human Ortholog file....");

    Iterator<?> tsvIter;
    try {
        tsvIter = FormattedTextParser.parseTabDelimitedReader(preader);
    } catch (Exception e) {
        throw new Exception("cannot parse file: " + preader.toString(), e);
    }

    while (tsvIter.hasNext()) {

        String[] line = (String[]) tsvIter.next();

        if (line.length < 4) {
            LOG.error("Couldn't process line. Expected 4 cols, but was " + line.length);
            continue;
        }

        String humanIdentifier = line[0].trim();
        String xenopusIdentifier = line[1].trim().substring(12);

        if (StringUtils.isEmpty(xenopusIdentifier) || StringUtils.isEmpty(humanIdentifier)) {
            continue;
        }

        String gene2 = getGene(humanIdentifier, "9606");

        HashSet geneIds = genesPageName.get(xenopusIdentifier);
        Iterator it = geneIds.iterator();

        while (it.hasNext()) {

            String geneId = (String) it.next();
            Item gene1 = genes.get(geneId);
            if (gene1 != null && gene2 != null) { //lot of trouble..why should this check be required..does not make sense..spend time debug
                processHomologues(gene1.getIdentifier(), gene2);
            }

        }

    }

    preader.close();

}

From source file:org.intermine.bio.dataconversion.XenmineConverter.java

/**
 * /*  w w  w  . j  a v a 2  s  .  c  o m*/
 * @param reader
 * @throws Exception
 * @throws ObjectStoreException
 */

private void processMouseOrthologFile(Reader preader) throws Exception, ObjectStoreException {

    /* entrez/NCBI gene ID     
     * Xenbase GenePage     
     * symbol
     * name
     */

    System.out.println("Processing Mouse Ortholog file....");

    Iterator<?> tsvIter;
    try {
        tsvIter = FormattedTextParser.parseTabDelimitedReader(preader);
    } catch (Exception e) {
        throw new Exception("cannot parse file: " + preader.toString(), e);
    }

    while (tsvIter.hasNext()) {

        String[] line = (String[]) tsvIter.next();

        if (line.length < 4) {
            LOG.error("Couldn't process line. Expected 4 cols, but was " + line.length);
            continue;
        }

        String mouseIdentifier = line[0].trim();
        String xenopusIdentifier = line[1].trim().substring(12);

        if (StringUtils.isEmpty(xenopusIdentifier) || StringUtils.isEmpty(mouseIdentifier)) {
            continue;
        }

        String gene2 = getGene(mouseIdentifier, "10090");

        HashSet geneIds = genesPageName.get(xenopusIdentifier);
        Iterator it = geneIds.iterator();

        while (it.hasNext()) {

            String geneId = (String) it.next();
            Item gene1 = genes.get(geneId);
            if (gene1 != null && gene2 != null) { //lot of trouble..why should this check be required..does not make sense..spend time debug
                processHomologues(gene1.getIdentifier(), gene2);
            }

        }

    }

    preader.close();

}