GOgetter (no merge)
Created: 2016-06-10 12:02:24
Retrieves all GO terms (with experimental evidence) associated with the given genelist. The GO terms are returned in a list per gene.
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Workflow Components
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Authors (1)
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Titles (1)
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Descriptions (1)
Retrieves all GO terms (with experimental evidence) associated with the given genelist. The GO terms are returned in a list per gene. |
![header=[] body=[These are the listed dependencies of the workflow] cssheader=[boxoverTooltipHeader] cssbody=[boxoverTooltipBody] delay=[200] Information](/images/famfamfam_silk/information.png?1680607579)
Dependencies (0)
Inputs (2)
Name |
Description |
org |
KEGG organism code
|
genes |
List of gene IDs
|
Processors (12)
Name |
Type |
Description |
Get_GO |
rest |
|
Filter_list_by_uniprot_id |
localworker |
Scriptimport 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));
}
}
|
Get_KEGG |
rest |
|
Remove_String_Duplicates |
localworker |
ScriptList strippedlist = new ArrayList();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
if (strippedlist.contains(item) == false) {
strippedlist.add(item);
}
}
|
Split_by_newline |
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]);
}
}
|
find_uniprot_in_kegg |
beanshell |
ScriptStringBuilder builder = new StringBuilder();
String[] uitkomst = input.split("\n");
boolean found = false;
for (int x=0; x < uitkomst.length; x++)
{
if (uitkomst[x].contains("UniProt"))
{
found = true;
output = uitkomst[x];
}
}
if (! found) {
output = "";
}
|
regex_uniprot_id |
stringconstant |
Value[O,P,Q][0-9][A-Z,0-9]{3,}[0-9] |
0 |
stringconstant |
Value0 |
regex_newline |
stringconstant |
Value\n |
Remove_Header |
beanshell |
Scriptimport java.util.Arrays;
String[] list = input.split("\n");
String[] out = Arrays.copyOfRange(list, 1, list.length);
output = out; |
Merge_String_List_to_a_String |
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();
|
newline |
stringconstant |
Value
|
Beanshells (2)
Name |
Description |
Inputs |
Outputs |
find_uniprot_in_kegg |
|
input
|
output
|
Remove_Header |
|
input
|
output
|
Datalinks (14)
Source |
Sink |
Filter_list_by_uniprot_id:filteredlist |
Get_GO:id |
find_uniprot_in_kegg:output |
Filter_list_by_uniprot_id:stringlist |
regex_uniprot_id:value |
Filter_list_by_uniprot_id:regex |
0:value |
Filter_list_by_uniprot_id:group |
org |
Get_KEGG:org |
Split_by_newline:split |
Get_KEGG:id |
Remove_Header:output |
Remove_String_Duplicates:stringlist |
genes |
Split_by_newline:string |
regex_newline:value |
Split_by_newline:regex |
Get_KEGG:responseBody |
find_uniprot_in_kegg:input |
Get_GO:responseBody |
Remove_Header:input |
newline:value |
Merge_String_List_to_a_String:seperator |
Remove_String_Duplicates:strippedlist |
Merge_String_List_to_a_String:stringlist |
Merge_String_List_to_a_String:concatenated |
GO_List |
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Version 1
(of 1)
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Title: Description Needed
Rating:
not yet rated
Created: 2016-06-18 08:49:03
|
Updated: 2016-06-18 08:49:03
Hi Dave, I think a more detailed description of the workflow could clarify the use of Taverna for people who are not familiar with your application and Taverna. Thanks.
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