BiomartAndEMBOSSDisease
Created: 2011-07-12 12:54:05
Last updated: 2012-03-19 15:31:14
This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions with mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned.
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Authors (1)
Titles (1)
Descriptions (1)
This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions with mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned. |
Dependencies (0)
Processors (10)
Name |
Type |
Description |
GetUniqueHomolog |
beanshell |
ScriptList HSOut = new ArrayList();
List RatOut = new ArrayList();
List MouseOut = new ArrayList();
Map hsToMouse = new HashMap();
Iterator j = MouseGeneIDs.iterator();
for (Iterator i = HSGeneIDs.iterator(); i.hasNext();) {
String id = (String)i.next();
hsToMouse.put(id, j.next());
}
Map hsToRat = new HashMap();
j = RatGeneIDs.iterator();
for (Iterator i = HSGeneIDs.iterator(); i.hasNext();) {
String id = (String)i.next();
hsToRat.put(id, j.next());
}
// Build the unique outputs
for (Iterator i = hsToRat.keySet().iterator(); i.hasNext();) {
String hsID = (String)i.next();
String ratID = (String)hsToRat.get(hsID);
// Remove version number
// ratID = (ratID.split("."))[0];
String mouseID = (String)hsToMouse.get(hsID);
// Remove version number
//mouseId = (mouseID.split("."))[0];
if (ratID != null && mouseID != null && ratID.equals("")==false && mouseID.equals("")==false) {
HSOut.add(hsID);
RatOut.add(ratID.split("\\.")[0]);
MouseOut.add(mouseID.split("\\.")[0]);
}
} |
CreateFasta |
beanshell |
Scriptfasta = ">Human\n"+hsSeq+"\n>Mouse\n"+mmSeq+"\n>Rat\n"+rnSeq; |
FlattenImageList |
localworker |
Scriptflatten(inputs, outputs, depth) {
for (i = inputs.iterator(); i.hasNext();) {
element = i.next();
if (element instanceof Collection && depth > 0) {
flatten(element, outputs, depth - 1);
} else {
outputs.add(element);
}
}
}
outputlist = new ArrayList();
flatten(inputlist, outputlist, 1); |
plot |
soaplab |
Endpointhttp://www.ebi.ac.uk/soaplab/emboss4/services/alignment_multiple.prettyplot |
emma |
soaplab |
Endpointhttp://www.ebi.ac.uk/soaplab/emboss4/services/alignment_multiple.emma |
seqret |
soaplab |
Endpointhttp://www.ebi.ac.uk/soaplab/emboss4/services/edit.seqret |
getMMusSequence |
biomart |
|
getHSapSequence |
biomart |
|
getRNorSequence |
biomart |
|
hsapiens_gene_ensembl_2 |
biomart |
|
Beanshells (2)
Name |
Description |
Inputs |
Outputs |
GetUniqueHomolog |
|
HSGeneIDs
MouseGeneIDs
RatGeneIDs
|
HSOut
RatOut
MouseOut
|
CreateFasta |
|
hsSeq
mmSeq
rnSeq
|
fasta
|
Outputs (4)
Name |
Description |
outputPlot |
|
HSapIDs |
|
MMusIDs |
|
RNorIDs |
|
Datalinks (17)
Source |
Sink |
hsapiens_gene_ensembl_2:hsapiens_gene_ensembl.ensembl_gene_id |
GetUniqueHomolog:HSGeneIDs |
hsapiens_gene_ensembl_2:hsapiens_gene_ensembl.mouse_ensembl_gene |
GetUniqueHomolog:MouseGeneIDs |
hsapiens_gene_ensembl_2:hsapiens_gene_ensembl.rat_ensembl_gene |
GetUniqueHomolog:RatGeneIDs |
getMMusSequence:mmusculus_gene_ensembl.coding_gene_flank |
CreateFasta:mmSeq |
getHSapSequence:hsapiens_gene_ensembl.coding_gene_flank |
CreateFasta:hsSeq |
getRNorSequence:rnorvegicus_gene_ensembl.coding_gene_flank |
CreateFasta:rnSeq |
plot:Graphics_in_PNG |
FlattenImageList:inputlist |
emma:outseq |
plot:sequences_direct_data |
seqret:outseq |
emma:sequence_direct_data |
CreateFasta:fasta |
seqret:sequence_direct_data |
GetUniqueHomolog:MouseOut |
getMMusSequence:mmusculus_gene_ensembl.ensembl_gene_id_filter |
GetUniqueHomolog:HSOut |
getHSapSequence:hsapiens_gene_ensembl.ensembl_gene_id_filter |
GetUniqueHomolog:RatOut |
getRNorSequence:rnorvegicus_gene_ensembl.ensembl_gene_id_filter |
FlattenImageList:outputlist |
outputPlot |
GetUniqueHomolog:HSOut |
HSapIDs |
GetUniqueHomolog:MouseOut |
MMusIDs |
GetUniqueHomolog:RatOut |
RNorIDs |
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