BLAST-ClustalW workflow

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 baseUrl = "http://xml.nig.ac.jp/rest/Invoke";
String service = "Blast";
String method = "searchParam";
String program = "blastn";
String encode = "UTF8";

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

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

Value

Script

List accessionlist = new ArrayList();
List startList = new ArrayList();
List endList = new ArrayList();
int count=0;
for(Iterator i = blastresult.iterator(); i.hasNext();) {
	String[] line=((String)i.next()).split("\t");
	String accession = line[1].substring(0,line[1].indexOf('|'));
	if(accessionlist.contains(accession)){
		continue;
	}
	accessionlist.add(accession);
	startList.add(line[8]);
	endList.add(line[9]);
	count++;
	if(count>=10) {
		break;	
	}
}

		

Script

List url = new ArrayList();

String service = "GetEntry";
String method = "getDDBJEntry";

String baseUrl = "http://xml.ddbj.nig.ac.jp/rest/Invoke?";
baseUrl += "service=" + service
	+"&method=" + method
	+"&accession=";

for(Iterator i = accession.iterator(); i.hasNext();) {
   url.add(baseUrl+(String)i.next());
}

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 entry = "";

for(int i=0; i end){
		dna = dnaBuf.subSequence(end, start);
	}else{
		dna = dnaBuf.subSequence(start, end);
	}
	entry += ">" + accession + "|" + org + "\n" + dna + "\n";
}

Script

String output = "";

String encode = "UTF8";
String tmpQuery = URLEncoder.encode(query+"\n"+entry,encode);

String baseQuery = "service=ClustalW&method=analyzeSimple&query=" + tmpQuery;
String baseUrl = "http://xml.nig.ac.jp/rest/Invoke";

URL url = new URL(baseUrl);
URLConnection urlc = url.openConnection();

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

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

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

Value