gene subset extract
Created: 2011-03-29 14:55:31
Last updated: 2011-03-29 15:00:22
This workflow functions for matching a set of genes as a part of whole gene data set and aim to extract the subset as a separate list.
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Workflow Components
Authors (2)
Alan Williams |
Abd el naser El Ashry |
Titles (3)
RetryPolicyAdvantage |
Spread sheet matching for genes |
Retry_example |
Descriptions (3)
This workflow demonstrates the advantages of using the retry options for making your workflow more robust. The 'Sometimes_Fails' service is written to throw an error every so often. If the service is only invoked once for each iteration, it will therefore throw errors. If you change the retry policy to 3 or 5, it will almost always complete successfully |
This workflow functions for matching a set of genes as a part of whole gene data set and aim to extract the subset as a separate list. |
This workflow demonstrates the advantages of using the retry |
Dependencies (0)
Inputs (2)
Name |
Description |
file_url |
|
Gene_ID |
|
Processors (7)
Name |
Type |
Description |
SpreadsheetImport |
spreadsheet |
|
string2stringlist |
localworker |
ScriptList 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]);
}
}
|
regex_value |
stringconstant |
Value\n |
Beanshell |
beanshell |
ScriptString subset_input = subset.trim();
String whole_input = wholeset.trim();
String[] array = subset_input.split(",");
String matchedset = "";
if(array[1].equals("c"))
{
matchedset = "I found a C !!!!";
}
else
{
if(whole_input.contains(array[0]))
{
matchedset = whole_input;
}
else
{
matchedset = "Value not found!";
}
}
|
SpreadsheetImport_2 |
spreadsheet |
|
string2stringlist_2 |
localworker |
ScriptList 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]);
}
}
|
Merge_Strings |
localworker |
ScriptString seperatorString = "\n";
if (seperator != void) {
seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
sb.append(item);
if (i.hasNext()) {
sb.append(seperatorString);
}
}
concatenated = sb.toString();
|
Beanshells (1)
Name |
Description |
Inputs |
Outputs |
Beanshell |
|
subset
wholeset
|
matchedset
|
Outputs (5)
Name |
Description |
excel_output |
|
split |
|
subset_split |
|
matchedset |
|
single_list |
|
Datalinks (14)
Source |
Sink |
file_url |
SpreadsheetImport:fileurl |
regex_value:value |
string2stringlist:regex |
SpreadsheetImport:output |
string2stringlist:string |
string2stringlist_2:split |
Beanshell:subset |
string2stringlist:split |
Beanshell:wholeset |
Gene_ID |
SpreadsheetImport_2:fileurl |
regex_value:value |
string2stringlist_2:regex |
SpreadsheetImport_2:output |
string2stringlist_2:string |
Beanshell:matchedset |
Merge_Strings:stringlist |
SpreadsheetImport:output |
excel_output |
string2stringlist:split |
split |
string2stringlist_2:split |
subset_split |
Beanshell:matchedset |
matchedset |
Merge_Strings:concatenated |
single_list |
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License
All versions of this Workflow are
licensed under:
Version 1
(of 1)
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