Takes a list of external references to genes/proteins/metabolites, finds all pathways on WikiPathways that contain one of the given genes/proteins/metabolites and downloads them in a given file format.
String file_name = path_name + pathway_species + "_" + pathway_name;
pathway_name
path_name
pathway_species
file_name
String path_name = output_path + File.separatorChar +
xref + File.separatorChar;
output_path
xref
path_name
int count = list.size();
list
count
net.sourceforge.taverna.scuflworkers.io.TextFileReader
\n
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
http://www.myexperiment.org/workflows/106/download?version=1
0
http://www.myexperiment.org/workflows/392/download?version=2
http://www.myexperiment.org/workflows/391/download?version=2
The location of a text file containing on each line a gene/protein/metabolite identifier (e.g. P04637).
The path to write the downloaded pathway files to.
The type of the file to write. This can be one of:
- gpml (xml format, for use in WikiPathways, PathVisio, Cytoscape)
- png (rasterized image format)
- svg (vector image format)
- pdf (portable document format)
- pwf (for use in Eu.Gene)
- txt (a text file containing a list of external references for the genes/proteins/metabolites on the pathway)
A list of files that were written.