Sequence_or_ID

Created: 2008-06-01 14:15:12

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Given a sequence or sequence entry identifer (e.g. uniprot:wap_rat), return the sequence in fasta format.

If a sequence identifier, in database:identifier format, is input the EBI's WSDbfetch web service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) is used to retrive the sequence in fasta format. Otherwise the input is assumed to be a sequence and if passed through the Soaplab EMBOSS seqret service to force the sequence into fasta format.

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Workflow Components

Inputs (1)

Name	Description
Sequence_or_ID	Either an actual sequence or an entry identifer in database:identifier format (e.g. uniprot:wap_rat).

Processors (5)

Name	Type	Description
Is_sequence	beanshell	Return true if the input is a sequence or false if the input is a sequence identifer (e.g. uniprot:wap_rat).
Fail_if_identifer	local	Fails if the workflow input is an identifier (i.e. is an actual sequence).
Fail_if_sequence	local	Fails if the workflow input was a sequence (i.e. is an identifer).
fetchData	arbitrarywsdl	Fetch the sequence in fasta format from the identifer using EBI's WSDbfetch service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch).
seqret	soaplabwsdl	Format sequence into fasta format.

Beanshells (1)

Name	Description	Inputs	Outputs
Is_sequence	Return true if the input is a sequence or false if the input is a sequence identifer (e.g. uniprot:wap_rat).	sequence	is_sequence

Outputs (1)

Name	Description
Sequence	Sequence in fasta format.

Links (7)

Source	Sink
Sequence_or_ID	Is_sequence:sequence
Is_sequence:is_sequence	Fail_if_identifer:test
Is_sequence:is_sequence	Fail_if_sequence:test
Sequence_or_ID	fetchData:query
Sequence_or_ID	seqret:sequence_direct_data
fetchData:fetchDataReturn	Sequence
seqret:outseq	Sequence

Coordinations (2)

Controller	Target
Fail_if_sequence	fetchData
Fail_if_identifer	seqret

Information Workflow Type

Taverna 1

Information Uploader

Hamish McWilliam

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Hamish McWilliam

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Information Statistics

3431 viewings

2498 downloads

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Sequence_or_ID

Created by Hamish McWilliam on Sunday 01 June 2008 14:15:12 (UTC)

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