Homology workflow

Script

String baseUrl = "http://xml.nig.ac.jp/rest/Invoke";
String service = "ARSA";
String method = "searchByXMLPath";
String count = "100";
String offset = "1";
String encode = "UTF8";

String queryPath = "/ENTRY/DDBJ/division=='HUM' AND (/ENTRY/DDBJ/length>=300 AND /ENTRY/DDBJ/length<=1000) "
			+ "AND (/ENTRY/DDBJ/feature-table/feature{/f_key = 'CDS' AND "
			+ "/f_quals/qualifier{/q_name = 'gene' AND /q_value=='"
			+ geneName
			+ "'}})";
String returnPath = "/ENTRY/DDBJ/primary-accession";

//make url
String url = baseUrl + "?" + "queryPath=" + URLEncoder.encode(queryPath, encode)
		+ "&returnPath=" + URLEncoder.encode(returnPath, encode)
		+ "&service=" + URLEncoder.encode(service, encode)
		+ "&method=" + URLEncoder.encode(method, encode)
		+ "&count=" + URLEncoder.encode(count, encode)
		+ "&offset="+ URLEncoder.encode(offset, encode);

Script

URL inputURL = null;
if (base != void) {
  inputURL = new URL(new URL(base), url);
}
else {
  inputURL = new URL(url);
}
URLConnection con = inputURL.openConnection();
InputStream in = con.getInputStream();

InputStreamReader isr = new InputStreamReader(in);
Reader inReader = new BufferedReader(isr);

StringBuffer buf = new StringBuffer();
int ch;
while ((ch = inReader.read()) > -1) {
  buf.append((char)ch);
}
inReader.close();
contents = buf.toString();


//String NEWLINE = System.getProperty("line.separator");
//
//URL inputURL = null;
//if (base != void) {
//	inputURL = new URL(new URL(base), url);
//} else {
//	inputURL = new URL(url);
//}
//StringBuffer result = new StringBuffer();
//BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream()));
//String line = null;
//while ((line = reader.readLine()) != null) {
//	result.append(line);
//	result.append(NEWLINE);
//}
//
//contents = result.toString();

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

Script

String repAccession = (String)arsaResultLines.get(2);

Script

String baseUrl = "http://xml.nig.ac.jp/rest/Invoke";
String service = "GetEntry";
String method = "getFASTA_DDBJEntry";

String url = baseUrl 
	+"?service=" + service
	+"&method=" + method 
	+"&accession=" + accession;

Script

URL inputURL = null;
if (base != void) {
  inputURL = new URL(new URL(base), url);
}
else {
  inputURL = new URL(url);
}
URLConnection con = inputURL.openConnection();
InputStream in = con.getInputStream();

InputStreamReader isr = new InputStreamReader(in);
Reader inReader = new BufferedReader(isr);

StringBuffer buf = new StringBuffer();
int ch;
while ((ch = inReader.read()) > -1) {
  buf.append((char)ch);
}
inReader.close();
contents = buf.toString();


//String NEWLINE = System.getProperty("line.separator");
//
//URL inputURL = null;
//if (base != void) {
//	inputURL = new URL(new URL(base), url);
//} else {
//	inputURL = new URL(url);
//}
//StringBuffer result = new StringBuffer();
//BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream()));
//String line = null;
//while ((line = reader.readLine()) != null) {
//	result.append(line);
//	result.append(NEWLINE);
//}
//
//contents = result.toString();

Script

String service = "Blast";
String method = "searchParam";
String program = "blastn";
String encode = "UTF8";

String query = "service=" + service
	+"&method=" + method 
	+"&program=" + program
	+"&database=" + URLEncoder.encode(database,encode)
	+"&query=" + URLEncoder.encode(dnaSeq,encode)
	+"¶m=" + URLEncoder.encode(param,encode);

Script

URL url = new URL("http://xml.nig.ac.jp/rest/Invoke");

URLConnection urlc = url.openConnection();

urlc.setDoOutput(true);
urlc.setAllowUserInteraction(false);

PrintStream ps = new PrintStream(urlc.getOutputStream());
ps.print(query);
ps.close();

BufferedReader br = new BufferedReader(new InputStreamReader(urlc.getInputStream()));
StringBuffer sb = new StringBuffer();
String line = null;
while ((line = br.readLine()) != null) {
	sb.append(line + "\n");
}
String contents = sb.toString();
br.close();

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]);
	}
}

Script

//extract accession number and similariy from blast result.

ArrayList parsedBlastResult = new ArrayList();

for (int i = 0; i < lines.size(); i++) {
	String[] cols = lines.get(i).toString().split("\t");
	String accession = (String)cols[1].substring(0, cols[1].indexOf("|"));
	String[] accessionAndSimilarity = { accession, cols[2] };
	parsedBlastResult.add(accessionAndSimilarity);
}

result = parsedBlastResult.toArray();

Script

String baseUrl = "http://xml.nig.ac.jp/rest/Invoke";
String service = "ARSA";
String method = "searchByXMLPath";
String count = "100";
String offset = "1";
String encode = "UTF8";

String queryPath = "/ENTRY/DDBJ/primary-accession=='" + blastResult.get(0) + "'";
String returnPath = "/ENTRY/DDBJ/organism";

//make url
String url = baseUrl + "?" + "queryPath=" + URLEncoder.encode(queryPath, encode)
		+ "&returnPath=" + URLEncoder.encode(returnPath, encode)
		+ "&service=" + URLEncoder.encode(service, encode)
		+ "&method=" + URLEncoder.encode(method, encode)
		+ "&count=" + URLEncoder.encode(count, encode)
		+ "&offset="+ URLEncoder.encode(offset, encode);

Script

Hashtable organismAccession = new Hashtable();

for (int i = 0; i < organismNameResult.size(); i++) {
	String[] organismLines = organismNameResult.get(i).split("\n");
	String organism = organismLines[2];
	if (!organismAccession.containsKey(organism)) {
		organismAccession.put(organism, accessionAndSimilarity.get(i).get(0) + "\t" + accessionAndSimilarity.get(i).get(1));
	}
}

String[] keys = new String[organismAccession.size()];
Enumeration enu = organismAccession.keys();
int count = 0;
while (enu.hasMoreElements()) {
	keys[count] = (String) enu.nextElement();
	count++;
}
Arrays.sort(keys);
StringBuffer sb = new StringBuffer();
sb.append("DDBJ entries:\t" + arsaResultNum + "\n");
sb.append("Representative accession:\t" + representiveAccession + "\n");
sb.append("Organism name\tDDBJ accession number\tSequence similarity \n");
for (int i = 0; i < keys.length; i++) {
	sb.append(keys[i] + "\t" + (String)organismAccession.get(keys[i]) + "\n");
}
result = sb.toString();

Script

URL inputURL = null;
if (base != void) {
  inputURL = new URL(new URL(base), url);
}
else {
  inputURL = new URL(url);
}
URLConnection con = inputURL.openConnection();
InputStream in = con.getInputStream();

InputStreamReader isr = new InputStreamReader(in);
Reader inReader = new BufferedReader(isr);

StringBuffer buf = new StringBuffer();
int ch;
while ((ch = inReader.read()) > -1) {
  buf.append((char)ch);
}
inReader.close();
contents = buf.toString();


//String NEWLINE = System.getProperty("line.separator");
//
//URL inputURL = null;
//if (base != void) {
//	inputURL = new URL(new URL(base), url);
//} else {
//	inputURL = new URL(url);
//}
//StringBuffer result = new StringBuffer();
//BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream()));
//String line = null;
//while ((line = reader.readLine()) != null) {
//	result.append(line);
//	result.append(NEWLINE);
//}
//
//contents = result.toString();

Value

Value

Script

hitCount = (String)arsaResultLines.get(0).replaceAll("hitscount       =", "").trim();