DAS sequence retrieval

Created: 2011-05-30 01:20:35 Last updated: 2011-05-30 01:26:47

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Retrieve Protein or Genome sequences using the Distributed Annotation System (DAS).

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

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 reference source following this format "http://www.server.com/das/source/". Find a public list of available DAS reference 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. Do not specify to get the whole sequence.

Processors (2)

Name	Type	Description
Get_Sequence	rest
create_range	beanshell	Script String 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
Sequence_DAS_format
Service_status

Datalinks (7)

Source	Sink
ID	Get_Sequence:ID
create_range:range	Get_Sequence:range
DasSource	Get_Sequence:DasSource
start	create_range:start
stop	create_range:stop
Get_Sequence:responseBody	Sequence_DAS_format
Get_Sequence:status	Service_status

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Information Workflow Type

Taverna 2

Information Uploader

Rafael C. Jimenez

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Rafael C. Jimenez

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Information Statistics

1576 viewings

1288 downloads

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Version History

In chronological order:

DAS sequence retrieval

Created by Rafael C. Jimenez on Monday 30 May 2011 01:20:35 (UTC)
DAS sequence retrieval

Created by Rafael C. Jimenez on Monday 30 May 2011 01:26:46 (UTC)

Revision comment:

The workflow is the same. This new version includes more information describing the outputs.