Like any parser or exporter, you must follow the setup instructions for Entanglement BEFORE you begin.
Before using the parser be sure to download a flat file format of UniProt (any version).
You will then need to retrieve the source code for the Parser, which is available here. This can be done using the following commands:
git clone https://firstname.lastname@example.org/jmullen/uniprot-parser.git
Ensure you are connected to the couchDB server. You may now create a graph, simply by typing the following line of code into your terminal;
mvn exec:java -Dexec.mainClass=uk.ac.ncl.en_uniprot_importer.Main -Dexec.args="<dblocation> <numofproteins> <clustername> <cluster> <dbname> <graphname> <username> <password> <subsize>"
Where the Dexec.args refer to:
- dblocation = location of the Uniprot.dat flat file on your local machine
- numofproteins = number of proteins you wish to parse into Entanglement
- clustername = the name of your cluster e.g. “local”
- cluster = your cluster host:port e.g. “localhost:5984
- dbname = the name you wish to give your database
- graphname = the name you wish to give your graph
- username = your couchDB username
- password = the password of you couchDB account
- subsize = the size of your transactions
After running the parser you will end up with a graph database that looks like this;