pathway difference in ortholog genes
Created: 2016-06-10 08:21:03
Download WorkflowThis workflow looks at a set of human genes and search for the orthologs of mouse and rat.
Then it gets for all the genes the pathways linked to it in Kegg and search for difference in them.
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Workflow Components
Authors (1)
| Tom Rosman |
Titles (1)
| pathway difference in ortholog genes |
Descriptions (1)
| This workflow looks at a set of human genes and search for the orthologs of mouse and rat. Then it gets for all the genes the pathways linked to it in Kegg and search for difference in them. |
Dependencies (0)
None
Inputs (1)
| Name | Description |
|---|---|
| ID |
Processors (24)
| Name | Type | Description |
|---|---|---|
| REST_Service | rest | |
| split_tab | beanshell |
ScriptString[] split = in1.split("\\t");
out1 = split[1].replace("\n", ""); |
| REST_Kegg_getGenesOrthologen | rest | |
| getReal_ortholog | beanshell |
Scriptimport java.io.*;
import java.util.*;
String[] lines = in1.split("\\n");
ArrayList hsa = new ArrayList();
ArrayList mmu = new ArrayList();
ArrayList rno = new ArrayList();
for (String x : lines) {
String line = x.split("\\t")[1];
if (line.substring(0,3).equals("hsa")) {
hsa.add(line);
} else if (line.substring(0,3).equals("mmu")) {
mmu.add(line);
} else if (line.substring(0,3).equals("rno")) {
rno.add(line);
}
}
int index = hsa.indexOf("hsa:" + id);
String out_mmu;
String out_rno;
try {
out_mmu = mmu.get(index);
out_rno = rno.get(index);
} catch (java.lang.IndexOutOfBoundsException e) {
out_mmu = mmu.get(index-1);
out_rno = rno.get(index-1);
}
|
| Split_string_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]);
}
}
|
| REST_pathways | rest | |
| REST_pathways_2 | rest | |
| REST_pathways_3 | rest | |
| Merge_hsa | 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_mmu | 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_rno | 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();
|
| Filter_UniquePathways_2 | beanshell |
Scriptimport java.util.*;
String[] split = in1.split("\\n");
ArrayList allPath = new ArrayList();
for (String x : split) {
if (!x.isEmpty()) {
allPath.add((x.split("\\t")[1]));
}
}
HashSet out1 = new HashSet(allPath);
|
| Filter_UniquePathways | beanshell |
Scriptimport java.util.*;
String[] split = in1.split("\\n");
ArrayList allPath = new ArrayList();
for (String x : split) {
if (!x.isEmpty()) {
allPath.add((x.split("\\t")[1]));
}
}
HashSet out1 = new HashSet(allPath);
|
| Filter_UniquePathways_3 | beanshell |
Scriptimport java.util.*;
String[] split = in1.split("\\n");
ArrayList allPath = new ArrayList();
for (String x : split) {
if (!x.isEmpty()) {
allPath.add((x.split("\\t")[1]));
}
}
HashSet out1 = new HashSet(allPath);
|
| getPathway_difference | beanshell |
Scriptimport java.util.*;
String[] off = in_off.split("\\n");
String[] hsa = in_hsa.split("\\n");
ArrayList offList = new ArrayList();
ArrayList hsaList = new ArrayList();
ArrayList out_same = new ArrayList();
ArrayList out_diff = new ArrayList();
for (String x: off) {
offList.add(x.substring(8));
}
for (String x: hsa) {
hsaList.add(x.substring(8));
}
for (String x: hsa) {
if (offList.contains(x.substring(8))) {
out_same.add(x.substring(8));
} else {
out_diff.add(x.substring(5));
}
}
for (String x: off) {
if ( ! hsaList.contains(x.substring(8))) {
out_diff.add(x.substring(5));
}
}
|
| Merge_rno_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();
|
| Merge_mmu_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();
|
| Merge_hsa_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();
|
| getPathway_difference_2 | beanshell |
Scriptimport java.util.*;
String[] off = in_off.split("\\n");
String[] hsa = in_hsa.split("\\n");
ArrayList offList = new ArrayList();
ArrayList hsaList = new ArrayList();
ArrayList out_same = new ArrayList();
ArrayList out_diff = new ArrayList();
for (String x: off) {
offList.add(x.substring(8));
}
for (String x: hsa) {
hsaList.add(x.substring(8));
}
for (String x: hsa) {
if (offList.contains(x.substring(8))) {
out_same.add(x.substring(8));
} else {
out_diff.add(x.substring(5));
}
}
for (String x: off) {
if ( ! hsaList.contains(x.substring(8))) {
out_diff.add(x.substring(5));
}
}
|
| getGene_in_pathway | beanshell |
Scriptimport java.util.*;
String[] splitGene = in_gene.split("\n");
String[] splitPway = in_pway.split("\n");
String gene;
String pway;
ArrayList pwayGene = new ArrayList();
for (String x : splitPway) {
pwayGene.add(x + "+");
}
for ( String x : splitGene ) {
if ( x.isEmpty() ) {
} else {
gene = x.split("\\t")[0];
pway = x.split(":")[2];
}
int nr = 0;
A: for (String y : pwayGene) {
String z = y.split("\\+")[0];
if (z.equals(pway.substring(3))) {
String newItem = pwayGene.get(nr) + gene.substring(4) + "+";
pwayGene.set(nr, newItem);
break A;
}
nr += 1;
}
}
|
| Merge_hsa_2_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();
|
| Merge_mmu_2_2_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();
|
| 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_getImage | rest |
Beanshells (8)
| Name | Description | Inputs | Outputs |
|---|---|---|---|
| split_tab | in1 | out1 | |
| getReal_ortholog |
in1 id |
out_rno out_mmu |
|
| Filter_UniquePathways_2 | in1 | out1 | |
| Filter_UniquePathways | in1 | out1 | |
| Filter_UniquePathways_3 | in1 | out1 | |
| getPathway_difference |
in_off in_hsa |
out_diff out_same |
|
| getPathway_difference_2 |
in_off in_hsa |
out_diff out_same |
|
| getGene_in_pathway |
in_gene in_pway |
pwayGene |
Outputs (7)
| Name | Description |
|---|---|
| out_orth_rno | |
| out_orth_mmu | |
| out_path_diff_mmu | |
| out_path_same_rno | |
| out_path_diff_rno | |
| out_pway_image | |
| out_path_same_mmu |
Datalinks (35)
| Source | Sink |
|---|---|
| Split_string_on_enter:split | REST_Service:id |
| REST_Service:responseBody | split_tab:in1 |
| split_tab:out1 | REST_Kegg_getGenesOrthologen:id |
| REST_Kegg_getGenesOrthologen:responseBody | getReal_ortholog:in1 |
| Split_string_on_enter:split | getReal_ortholog:id |
| ID | Split_string_on_enter:string |
| getReal_ortholog:out_rno | REST_pathways:id |
| getReal_ortholog:out_mmu | REST_pathways_2:id |
| Split_string_on_enter:split | REST_pathways_3:id |
| REST_pathways_3:responseBody | Merge_hsa:stringlist |
| REST_pathways_2:responseBody | Merge_mmu:stringlist |
| REST_pathways:responseBody | Merge_rno:stringlist |
| Merge_mmu:concatenated | Filter_UniquePathways_2:in1 |
| Merge_rno:concatenated | Filter_UniquePathways:in1 |
| Merge_hsa:concatenated | Filter_UniquePathways_3:in1 |
| Merge_hsa_2:concatenated | getPathway_difference:in_hsa |
| Merge_mmu_2:concatenated | getPathway_difference:in_off |
| Filter_UniquePathways:out1 | Merge_rno_2:stringlist |
| Filter_UniquePathways_2:out1 | Merge_mmu_2:stringlist |
| Filter_UniquePathways_3:out1 | Merge_hsa_2:stringlist |
| Merge_rno_2:concatenated | getPathway_difference_2:in_off |
| Merge_hsa_2:concatenated | getPathway_difference_2:in_hsa |
| Merge_hsa_2_2:concatenated | getGene_in_pathway:in_gene |
| Merge_mmu_2_2_2:concatenated | getGene_in_pathway:in_pway |
| Merge_hsa:concatenated | Merge_hsa_2_2:stringlist |
| getPathway_difference:out_same | Merge_mmu_2_2_2:stringlist |
| getGene_in_pathway:pwayGene | Split_enter:string |
| Split_enter:split | REST_Kegg_getImage:id |
| getReal_ortholog:out_rno | out_orth_rno |
| getReal_ortholog:out_mmu | out_orth_mmu |
| getPathway_difference:out_diff | out_path_diff_mmu |
| getPathway_difference_2:out_same | out_path_same_rno |
| getPathway_difference_2:out_diff | out_path_diff_rno |
| REST_Kegg_getImage:responseBody | out_pway_image |
| getPathway_difference:out_same | out_path_same_mmu |
Coordinations (0)
None
Workflow Type
Version 1
(of 1)
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