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.
Preview
Run
Run this Workflow in the Taverna Workbench...
Workflow Components
Authors (1)
Titles (1)
Descriptions (1)
Retrieves all GO terms (with experimental evidence) associated with the given genelist. The GO terms are returned in a list per gene. |
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 |
Uploader
License
All versions of this Workflow are
licensed under:
Version 1
(of 1)
Credits (2)
(People/Groups)
Attributions (0)
(Workflows/Files)
None
Shared with Groups (0)
None
Featured In Packs (0)
None
Log in to add to one of your Packs
Attributed By (0)
(Workflows/Files)
None
Favourited By (0)
No one
Statistics
By
|
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.
[ more ]
|
View
|
Other workflows that use similar services
(0)
There are no workflows in myExperiment that use similar services to this Workflow.
Comments (0)
No comments yet
Log in to make a comment