fetch_fasta
Created: 2009-03-20 11:22:45
Last updated: 2009-03-20 11:29:16
This work flow is designed to take an EMBL file containing the genomic data for an identified bacterium. From this information the workflow can determine whether or not that this strain is an MRSA type of bug. This can be determined based on the MecA profile of the given strain.
Blast is utilised to find a relationship with given proteins and that of know S. aureus strains. This phylogenic output is generated from a ClustalW algorithm that plots a phylogenic tree.
The output is presented in a pdf format detailing this strain. Details include: putative identification, presence of MecA and phylogenic tree and ID of it and its neighbour strains.
This workflow is useful as it can easily be adapted to other projects with only minor modification to its processes.
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Workflow Components
Inputs (3)
| Name |
Description |
| sequenceIds |
|
| query_strain_id |
|
| email |
|
Processors (18)
| Name |
Type |
Description |
| Get_Nucleotide_FASTA |
local |
|
| Write_Text_File |
local |
|
| run_blastall |
local |
|
| Read_FASTA |
local |
|
| splitIDs |
local |
|
| local_create_blastdb |
local |
|
| ClustalW |
local |
|
| Merge_FASTA |
local |
|
| create_blastall_cmd_args |
beanshell |
|
| create_formatdb_cmdArgs |
beanshell |
This beanshell will not be run until after the fasta file is written from the Write_Fasta_File processor.
This beanshell creates an array of strings (a list of plain text), with each element containing one element of the arguments for the formatdb command line. Note that you can change the text in the beanshell in the element in the line after the one containing "-n" to set the name of the blast database you want.
If you want to add any other command line arguments, follow the system in the beanshell. E.g. add the flag, e.g. "-x" in one line, and its argument "somethingOrOther" in another line. |
| parametersXML2 |
local |
|
| Neighbours |
local |
|
| getNeighbours |
arbitrarywsdl |
|
| addSequenceToFasta |
arbitrarywsdl |
|
| getSequences |
arbitrarywsdl |
|
| isMRSA |
workflow |
|
| EBI_TCoffee |
workflow |
|
| draw_tree |
local |
|
Beanshells (2)
| Name |
Description |
Inputs |
Outputs |
| create_blastall_cmd_args |
|
|
cmdArgsList
|
| create_formatdb_cmdArgs |
This beanshell will not be run until after the fasta file is written from the Write_Fasta_File processor.
This beanshell creates an array of strings (a list of plain text), with each element containing one element of the arguments for the formatdb command line. Note that you can change the text in the beanshell in the element in the line after the one containing "-n" to set the name of the blast database you want.
If you want to add any other command line arguments, follow the system in the beanshell. E.g. add the flag, e.g. "-x" in one line, and its argument "somethingOrOther" in another line. |
|
cmdArgsList
|
Outputs (5)
| Name |
Description |
| nuc_fasta |
|
| alignment |
|
| isMRSA |
|
| Neighbours |
|
| tree |
|
Links (16)
| Source |
Sink |
| Get_Nucleotide_FASTA:outputText |
Merge_FASTA:stringlist |
| Merge_FASTA:concatenated |
Write_Text_File:filecontents |
| create_blastall_cmd_args:cmdArgsList |
run_blastall:args |
| create_formatdb_cmdArgs:cmdArgsList |
local_create_blastdb:args |
| sequenceIds |
splitIDs:string |
| parametersXML2:output |
getSequences:parameters |
| query_strain_id |
isMRSA:sequenceId |
| Read_FASTA:filecontents |
EBI_TCoffee:Sequences |
| email |
EBI_TCoffee:Email_address |
| getNeighbours:parameters |
Neighbours:input |
| splitIDs:split |
Get_Nucleotide_FASTA:id |
| ClustalW:result |
tree |
| EBI_TCoffee:TCoffee_alignment |
alignment |
| Merge_FASTA:concatenated |
nuc_fasta |
| Neighbours:return |
Neighbours |
| isMRSA:isMRSA |
isMRSA |
Coordinations (9)
| Controller |
Target |
| Write_Text_File |
create_formatdb_cmdArgs |
| local_create_blastdb |
run_blastall |
| run_blastall |
parametersXML2 |
| getSequences |
Read_FASTA |
| addSequenceToFasta |
Read_FASTA |
| run_blastall |
addSequenceToFasta |
| run_blastall |
getNeighbours |
| Read_FASTA |
ClustalW |
| ClustalW |
draw_tree |
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Hi,
I think you may have some nested workflows in there that have not been uploaded (red boxes). Could you please check it and save it, choosing to embed the nested workflows?
cheers,
Paul