Get from a Pathway the Go fucntion from Kegg
Created: 2016-06-10 08:43:20
This workflow gets from a Pathway nr the Go term from the Kegg database and then looks up the go function in the AMIGO database.
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Workflow Components
Authors (1)
Titles (1)
Get from a Pathway the Go fucntion from Kegg |
Descriptions (1)
This workflow gets from a Pathway nr the Go term from the Kegg database and then looks up the go function in the AMIGO database. |
Dependencies (0)
Inputs (1)
Name |
Description |
pathwayNR |
Pathway input are the ko Pathway numbers from the Kegg database.
|
Processors (13)
Name |
Type |
Description |
Split_enter |
localworker |
ScriptList split = new ArrayList();
if (!string.equals("")) {
String regexString = "\n";
if (regex != void) {
regexString = regex;
}
String[] result = string.split(regexString);
for (int i = 0; i < result.length; i++) {
split.add(result[i]);
}
}
|
REST_Kegg_ko |
rest |
|
Filter_List_of_Strings_by_regex |
localworker |
Scriptfilteredlist = new ArrayList();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
if (item.matches(regex)) {
filteredlist.add(item);
}
}
|
Split_enter_2 |
localworker |
ScriptList split = new ArrayList();
if (!string.equals("")) {
String regexString = "\n";
if (regex != void) {
regexString = regex;
}
String[] result = string.split(regexString);
for (int i = 0; i < result.length; i++) {
split.add(result[i]);
}
}
|
Text_regex |
stringconstant |
Value.*GO:.* |
Filter_GoTerms |
beanshell |
ScriptString go = in1.trim();
String[] goSplit = go.split(" ");
String out1 = "";
boolean first = true;
for (String x : goSplit ) {
if (first) {
first = false;
} else {
out1 += "GO:"+ x + "\n";
}
} |
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();
|
Merge_String_List_to_a_String_2 |
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();
|
Text_regex_1 |
stringconstant |
ValueG.* |
Filter_list_of_strings_extracting_match_to_a_regex |
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));
}
}
|
Text_group_1 |
stringconstant |
Value0 |
Split_on_enter |
localworker |
ScriptList split = new ArrayList();
if (!string.equals("")) {
String regexString = "\n";
if (regex != void) {
regexString = regex;
}
String[] result = string.split(regexString);
for (int i = 0; i < result.length; i++) {
split.add(result[i]);
}
}
|
Workflow1 |
workflow |
|
Beanshells (2)
Name |
Description |
Inputs |
Outputs |
Filter_GoTerms |
|
in1
|
out1
|
Beanshell |
|
in1
|
out1
|
Outputs (2)
Name |
Description |
Go |
|
go_function |
|
Datalinks (15)
Source |
Sink |
pathwayNR |
Split_enter:string |
Split_enter:split |
REST_Kegg_ko:id |
Split_enter_2:split |
Filter_List_of_Strings_by_regex:stringlist |
Text_regex:value |
Filter_List_of_Strings_by_regex:regex |
REST_Kegg_ko:responseBody |
Split_enter_2:string |
Filter_List_of_Strings_by_regex:filteredlist |
Filter_GoTerms:in1 |
Filter_GoTerms:out1 |
Merge_String_List_to_a_String:stringlist |
Filter_list_of_strings_extracting_match_to_a_regex:filteredlist |
Merge_String_List_to_a_String_2:stringlist |
Merge_String_List_to_a_String:concatenated |
Filter_list_of_strings_extracting_match_to_a_regex:stringlist |
Text_regex_1:value |
Filter_list_of_strings_extracting_match_to_a_regex:regex |
Text_group_1:value |
Filter_list_of_strings_extracting_match_to_a_regex:group |
Merge_String_List_to_a_String_2:concatenated |
Split_on_enter:string |
Split_on_enter:split |
Workflow1:id |
Merge_String_List_to_a_String_2:concatenated |
Go |
Workflow1:go_pathway |
go_function |
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licensed under:
Version 1
(of 1)
Credits (2)
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Attributions (1)
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Favourited By (0)
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