KEGG:Get PW for met
Created: 2016-06-21 19:06:49
The purpose of the workflow is to retrieve all the pathways that the input metabolite(s) participates in.
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Authors (1)
Harish Dharuri
Kristina Hettne |
Titles (1)
Descriptions (1)
The purpose of the workflow is to retrieve all the pathways that the input metabolite(s) participates in. |
Dependencies (0)
Inputs (1)
Name |
Description |
compound_id |
The input for the workflow is a Kegg compound ID.
|
Processors (4)
Name |
Type |
Description |
get_compound_info |
rest |
Use the KEGG API to query the KEGG database for compound information. |
extract_pathway_from_compounds_file |
beanshell |
Shell script to extract pathways from compounds file. Scriptimport java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.ArrayList;
import java.util.Iterator;
String PATHWAY_Line;
List out1 = new ArrayList();
//First grab the line that contains the word "PATHWAY"
String p = "PATHWAY\\s+(.+?)\\b[A-Z]+?\\b\\s+";
Pattern pattern = Pattern.compile(p,Pattern.DOTALL);
Matcher matcher = pattern.matcher(in1);
while (matcher.find()){
PATHWAY_Line = matcher.group(1);
}
//Now get all the pathway ids from the "PATHWAY" line
String p1 = "(map[0-9]{5})";
Pattern pattern1 = Pattern.compile(p1,Pattern.MULTILINE);
Matcher matcher1 = pattern1.matcher(PATHWAY_Line);
while (matcher1.find()){
out1.add(matcher1.group(1));
}
|
Split_string_into_string_list_by_regular_expression |
localworker |
Split the input list on the newline character (this can be changed in the text constant input value). 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 |
Input constant for split method, can be changed (default is newline character \n). Value\n |
Beanshells (1)
Name |
Description |
Inputs |
Outputs |
extract_pathway_from_compounds_file |
Shell script to extract pathways from compounds file. |
in1
|
out1
|
Outputs (1)
Name |
Description |
output_pathways |
Output KEGG pathway identifiers
|
Datalinks (5)
Source |
Sink |
Split_string_into_string_list_by_regular_expression:split |
get_compound_info:query |
get_compound_info:responseBody |
extract_pathway_from_compounds_file:in1 |
regex_value:value |
Split_string_into_string_list_by_regular_expression:regex |
compound_id |
Split_string_into_string_list_by_regular_expression:string |
extract_pathway_from_compounds_file:out1 |
output_pathways |
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