Mining the Kegg pathway database with the top hits from a GWAS, thereby predicting which gene regulatory pathways may be altered as a result of genetic mutations in a subpopulation.

Script

import java.util.*;

String [] line = string.split("\t");
out1=line[0].trim();

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

flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);

Script

flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);

Script

import java.util.*;

List tmp_end = new ArrayList();
List tmp_start = new ArrayList();
width =Integer.parseInt(in1.get(0));

int out_end=0;
int out_start=0;
for(int i=0; i < in2.size(); i++) {
           value_pos = Integer.parseInt(in2.get(i));
	   out_end = value_pos + width;
	   out_start = value_pos - width;	
	

		
    tmp_end.add(out_end);
    tmp_start.add(out_start);
 }

end_out = tmp_end;
start_out = tmp_start;
chr_out = chr_in;

Script

BufferedReader getReader (String fileUrl, String encoding) throws IOException {
		InputStreamReader reader;
		try {
			if (encoding == null) {
				reader = new FileReader(fileUrl);
			} else {
				reader = new InputStreamReader(new FileInputStream(fileUrl),encoding); 
			}
		}
		catch (FileNotFoundException e) {
			// try a real URL instead
			URL url = new URL(fileUrl);
			if (encoding == null) {
				reader = new InputStreamReader (url.openStream());
			} else {
				reader = new InputStreamReader (url.openStream(), encoding);
			}
		}
		return new BufferedReader(reader);
	}



StringBuffer sb = new StringBuffer(4000);

if (encoding == void) {
	encoding = null;
}

BufferedReader in = getReader(fileurl, encoding);
String str;
String lineEnding = System.getProperty("line.separator");

while ((str = in.readLine()) != null) {
	sb.append(str);
	sb.append(lineEnding);
}
in.close();
filecontents = sb.toString();
  

Script

File f = File.createTempFile("taverna", ".tmp");

BufferedWriter writer = new BufferedWriter(new FileWriter(f));
writer.write(content);
writer.close();

filepath = f.getCanonicalPath();

Script

BufferedReader getReader (String fileUrl) throws IOException {
		InputStreamReader reader;
		try {
			reader = new FileReader(fileUrl);
		}
		catch (FileNotFoundException e) {
			// try a real URL instead
			URL url = new URL(fileUrl);
			reader = new InputStreamReader (url.openStream());
		}
		return new BufferedReader(reader);
	}

String NEWLINE = System.getProperty("line.separator");

boolean displayResults = false;
if (displayresults != void) {
	displayResults = Boolean.valueOf(displayresults).booleanValue();
}

StringBuffer sb = new StringBuffer(2000);

if (outputfile == void) {
	throw new RuntimeException("The 'outputfile' parameter cannot be null");
}

if (filelist == null) {
	throw new RuntimeException("The 'filelist' parameter cannot be null");
}

String str = null;

Writer writer = new FileWriter(outputfile);
for (int i = 0; i < filelist.size(); i++) {
	BufferedReader reader = getReader(filelist.get(i));
	while ((str = reader.readLine()) != null) {
		writer.write(str);
		writer.write(NEWLINE);

		if (displayResults) {
			sb.append(str);
			sb.append(NEWLINE);
		}
	}

	reader.close();

}
writer.flush();
writer.close();

if (displayResults) {
	results= sb.toString();
}

Script

if (infilename.equals(outfilename)) outfilename="output_" + outfilename;

Script

flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);