Get homologous from NCBI homoloGene

Script

        Map protein2group = new HashMap();
        Map protein2taxonomy = new HashMap();
        HashMap group2protein = new HashMap();

        URL url = null;
        BufferedReader reader = null;
        try {
            url = new URL(homologeneUrlNCBI);
            reader = new BufferedReader(new InputStreamReader(url.openStream()));
        } catch ( MalformedURLException e ) {
            e.printStackTrace();
        } catch ( IOException e ) {
            e.printStackTrace();
        }

        //read each line of text file
        String line = null;
        try {
            while((line = reader.readLine()) != null){
                if(line.length() > 1){
                    String[] el = line.split("\t");
                    String group = el[0];
                    String taxonomy = el[1];
                    String accession = el[5];

                    protein2group.put(accession,group);
                    protein2taxonomy.put(accession,taxonomy);
                    if(group2protein.containsKey(group)){
                        ((ArrayList) group2protein.get(group)).add(accession);
                    } else {
                        List accList = new ArrayList();
                        accList.add(accession);
                        group2protein.put(group,accList);
                    }

                }
            }
        } catch ( IOException e ) {
            e.printStackTrace();
        }


        /* Find homologs */
        //List queryAccs = new ArrayList();
        //queryAccs.add("XP_524741.2");
        //queryAccs.add("NP_001003746.1");
        //String specie = "9606";
        List listOfResults = new ArrayList();


        for(Object acc:queryAccs){
            String group = (String) protein2group.get(acc);
            List results = new ArrayList();
            if(group == null){
                // No homologous for this acc
            } else {
                List homologs = (List) group2protein.get(group);
                if(specie.equalsIgnoreCase("all")){
                    results.addAll(homologs);
                } else {
                    for(Object homolog:homologs){
                        if(((String)protein2taxonomy.get(homolog)).equalsIgnoreCase(specie)){
                            results.add(homolog);
                        }
                    }
                }
            }
            listOfResults.add(results);
        }

Value

Script

List split = new ArrayList();
if (!string.equals("")) {
	String regexString = ",";
	if (regex != void) {
		regexString = regex;
	}
	String[] result = string.split(regexString);
	for (int i = 0; i < result.length; i++) {
		split.add(result[i]);
	}
}

Value