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Kegg pathway diagrams

Created: 2010-03-19 12:41:27 Last updated: 2010-03-19 12:41:28

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Find pathways in which all the genes in the list are involved. Find all enzymes from the list of genes. For each pathway draw the diagram and colour the enzymes boxes in the colours specified.

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Authors (1)

Titles (2)

Descriptions (3)

Dependencies (0)

Inputs (4)

Name	Description
gene_ids	A list of KEGG gene ids
Species	KEGG The three letter species code The three letter species code used by KEGG
bg_color	The background colour for the boxes containing enzymes. The background colour for the boxes containing enzymes. Values can be given as strings or hexadecimal RGB colour codes.
fg_color	The text colour for the boxes containing enzymes. Values can be given as strings or hexadecimal RGB colour codes.

Processors (9)

Name	Type	Description
Workflow89	workflow
Get_Image_From_URL_2	localworker	Script URL inputURL = null;if (base != void) { inputURL = new URL(new URL(base), url);} else { inputURL = new URL(url);}byte[] contents;if (inputURL.openConnection().getContentLength() == -1) { // Content size unknown, must read first... byte[] buffer = new byte[1024]; int bytesRead = 0; int totalBytesRead = 0; InputStream is = inputURL.openStream(); while (bytesRead != -1) { totalBytesRead += bytesRead; bytesRead = is.read(buffer, 0, 1024); } contents = new byte[totalBytesRead];} else { contents = new byte[inputURL.openConnection().getContentLength()];}int bytesRead = 0;int totalBytesRead = 0;InputStream is = inputURL.openStream();while (bytesRead != -1) { bytesRead = is.read(contents, totalBytesRead, contents.length - totalBytesRead); totalBytesRead += bytesRead; if (contents.length==totalBytesRead) break;}image = contents;
color_pathway_by_objects	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation color_pathway_by_objects
get_enzymes_by_gene	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation get_enzymes_by_gene
get_genes_by_enzyme	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation get_genes_by_enzyme
get_pathways_by_genes	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation get_pathways_by_genes
Flatten_List	localworker	Script flatten(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);
Flatten_List_2	localworker	Script flatten(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);
Remove_String_Duplicates	localworker	Script List strippedlist = new ArrayList();for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); if (strippedlist.contains(item) == false) { strippedlist.add(item); }}

Beanshells (0)

Outputs (6)

Name	Description
KeggPathwayIDs	A list of the pathways found.
keggimageurl	The URLs of the images produced for the KeggImage output. The URLs of the images produced for the KeggImage output
keggGeneNames	A list of the gene ids, that was given as input with the species code concatenated.
coloured_images	List of pathway diagram with enzyme boxes coloured in specified colours
enzyme_list	List of enzyme id retrieve from Kegg using get_enzymes_by_gene
genes_list	List of ids that are enzymes

Datalinks (20)

Source	Sink
Species	Workflow89:part1
gene_ids	Workflow89:part2
color_pathway_by_objects:return	Get_Image_From_URL_2:url
get_pathways_by_genes:return	color_pathway_by_objects:pathway_id
Remove_String_Duplicates:strippedlist	color_pathway_by_objects:object_id_list
bg_color	color_pathway_by_objects:bg_color_list
fg_color	color_pathway_by_objects:fg_color_list
Workflow89:string	get_enzymes_by_gene:genes_id
Species	get_genes_by_enzyme:org
Flatten_List:outputlist	get_genes_by_enzyme:enzyme_id
Workflow89:string	get_pathways_by_genes:genes_id_list
get_enzymes_by_gene:return	Flatten_List:inputlist
get_genes_by_enzyme:return	Flatten_List_2:inputlist
Flatten_List_2:outputlist	Remove_String_Duplicates:stringlist
get_pathways_by_genes:return	KeggPathwayIDs
color_pathway_by_objects:return	keggimageurl
Workflow89:string	keggGeneNames
Get_Image_From_URL_2:image	coloured_images
Flatten_List:outputlist	enzyme_list
Remove_String_Duplicates:strippedlist	genes_list

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Jannetta

Information License

All versions of this Workflow are licensed under:

Information Version 1 (earliest) (of 3)

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Information Statistics

3247 viewings

1829 downloads

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Version History

In chronological order:

Kegg pathway diagrams with enzymes coloured

Created by Jannetta on Sunday 14 March 2010 13:56:02 (UTC)
Kegg pathway diagrams

Created by Jannetta on Wednesday 17 March 2010 14:44:44 (UTC)

Revision comment:

Changed colour input to take single inputs and create a list of colours equivalent in length to the gene list. All genes identified will be coloured on the Kegg diagram in the same colour.
Kegg pathway diagrams

Created by Jannetta on Friday 19 March 2010 12:41:27 (UTC)

Revision comment:

Flatten output values

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Kegg pathway diagrams

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