DAS features retrieval
Created: 2011-06-01 17:10:43
Last updated: 2011-06-01 17:57:45
Retrieve Protein or Genome features (annotations) using the Distributed Annotation System (DAS).
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Descriptions (1)
| Retrieve Protein or Genome features (annotations) using the Distributed Annotation System (DAS). |
Dependencies (0)
Inputs (4)
| Name |
Description |
| ID |
You can use different types of IDs depending on the DAS coordinate system (http://www.dasregistry.org/help_coordsys.jsp) you decided to use. If you selected a DAS source of type "Protein Sequence" and authority "UniProt" you could use UniProt (TrEMBL and SwissProt) accessions. For instance "P37173". If you selected a DAS source of type "Chromosome", authority "GRCh_37" and organism "Homo sapiens" you could use a chromosome ID. For instance "1".
|
| DasSource |
Input a DAS annotation source following this format "http://www.server.com/das/source/". Find a public list of available DAS annotation sources providing sequence information in the DAS registry … http://www.dasregistry.org/listSources.jsp … or create your own DAS source with easyDAS … http://www.ebi.ac.uk/panda-srv/easydas/
|
| start |
The start and stop attributes indicate the range of the segment to query. In this workflow is optional. Set an empty value to get the whole sequence.
|
| stop |
The start and stop attributes indicate the range of the segment to query. In this workflow is optional. Set an empty value to get the whole sequence.
|
Processors (2)
| Name |
Type |
Description |
| Get_Features |
rest |
|
| create_range |
beanshell |
ScriptString range = "";
if (!start.equals("") && !start.equals("")) {
if(Integer.parseInt(start) < Integer.parseInt(stop)){
range = ":" + start + "," + stop;
}
} |
Beanshells (1)
| Name |
Description |
Inputs |
Outputs |
| create_range |
|
start
stop
|
range
|
Outputs (2)
| Name |
Description |
| Features_DAS_format |
Have a look to the specification to know more about the DAS format ... http://www.biodas.org/documents/spec-1.6.html#features
|
| Service_status |
HTTP response status codes ... http://en.wikipedia.org/wiki/List_of_HTTP_status_codes
|
Datalinks (7)
| Source |
Sink |
| ID |
Get_Features:ID |
| create_range:range |
Get_Features:range |
| DasSource |
Get_Features:DasSource |
| start |
create_range:start |
| stop |
create_range:stop |
| Get_Features:responseBody |
Features_DAS_format |
| Get_Features:status |
Service_status |
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