ImportRefSeqtoKegg
Created: 2012-11-12 14:31:05
Last updated: 2013-01-08 09:25:20
This workflow extracts a column of RefSeq gene IDs from a CSV file and then converts them to Kegg gene identifiers. This workflow uses the new KEGG REST service, which replaces the old SOAP interface from 31st December 2012
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Workflow Components
Authors (1)
Titles (1)
Descriptions (1)
| This workflow extracts a column of RefSeq gene IDs from a CSV file and then converts them to Kegg gene identifiers. This workflow uses the new KEGG REST service, which replaces the old SOAP interface from 31st December 2012 |
Dependencies (0)
Inputs (1)
| Name |
Description |
| genes |
Accepts a CSV file with gene identifiers in one of the columns
An example input file can be found here: http://www.myexperiment.org/files/661.html
Please download and save it as .csv
|
Processors (11)
| Name |
Type |
Description |
| SpreadsheetImport |
spreadsheet |
|
| mmusculus_gene_ensembl |
biomart |
|
| Merge_gene_list |
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();
|
| add_unigene_to_string |
beanshell |
ScriptString[] split = input.split("\n");
Vector nonEmpty = new Vector();
for (int i = 0; i < split.length; i++)
{
String trimmed = split[i].trim();
nonEmpty.add(trimmed);
}
String output = "";
for (int i = 0; i < nonEmpty.size(); i++)
{
output = output + "unigene:" + (String) (nonEmpty.elementAt(i) + "\n");
} |
| Split_gene_list |
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]);
}
}
|
| regex_value |
stringconstant |
Value\n |
| bconvREST |
rest |
|
| target_value |
stringconstant |
Valuemmu |
| ExtractGene |
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));
}
}
|
| regex_value_1 |
stringconstant |
Valuemmu:[0-9]{4,} |
| group_value |
stringconstant |
Value0 |
Beanshells (1)
| Name |
Description |
Inputs |
Outputs |
| add_unigene_to_string |
|
input
|
output
|
Outputs (2)
| Name |
Description |
| Gene_List |
|
| KeggGeneIDs |
|
Datalinks (13)
| Source |
Sink |
| genes |
SpreadsheetImport:fileurl |
| SpreadsheetImport:D |
mmusculus_gene_ensembl:mmusculus_gene_ensembl.refseq_mrna_filter |
| mmusculus_gene_ensembl:mmusculus_gene_ensembl |
Merge_gene_list:stringlist |
| Merge_gene_list:concatenated |
add_unigene_to_string:input |
| add_unigene_to_string:output |
Split_gene_list:string |
| regex_value:value |
Split_gene_list:regex |
| Split_gene_list:split |
bconvREST:source |
| target_value:value |
bconvREST:target |
| regex_value_1:value |
ExtractGene:regex |
| group_value:value |
ExtractGene:group |
| bconvREST:responseBody |
ExtractGene:stringlist |
| Merge_gene_list:concatenated |
Gene_List |
| ExtractGene:filteredlist |
KeggGeneIDs |
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licensed under:
Version 3 (latest)
(of 3)
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Hi Katy, Can you add an example csv file pleae? I tried several inputs but all returned empty results for me. Thanks! -- Jun