Microbial Metagenomic Trait Calculation and Statistical Analysis Workflow

Script

url_query_string = "customer=anonymous" + "&sample_label=" + sample_label + "&sample_name=" + sample_name + "&sample_description=" + sample_description + "&mg_url=" + url + "&sample_environment=" + environment;

Value

Value

Script

import java.util.regex.*;

filteredlist = new ArrayList();
Pattern thePat = Pattern.compile(regex);
int theGroup = Integer.parseInt(group);

for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	Matcher matcher = thePat.matcher(item);

	if (matcher.find()) {
		filteredlist.add(matcher.group(theGroup));
	}
}

Script

String last = string.substring(string.lastIndexOf('/') + 1);

Script

import java.util.ArrayList;

ArrayList pass_flags = new ArrayList();
ArrayList fail_flags = new ArrayList();

if (condition.equals("0")) {
	pass_flags.add(condition);	
} else {
	fail_flags.add(condition);	
}

Script

String regexString = "\n";
String[] result = string.split(regexString);

String regexString1 = ",";
String[] result1 = result[1].split(regexString1);
result1[5] = result1[5].replace("\"","");

returnCode = result1[5];

Script

full_mg_list = mg_list + mg_jobid;